Starting phenix.real_space_refine on Wed Feb 14 09:39:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz5_27789/02_2024/8dz5_27789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz5_27789/02_2024/8dz5_27789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz5_27789/02_2024/8dz5_27789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz5_27789/02_2024/8dz5_27789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz5_27789/02_2024/8dz5_27789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz5_27789/02_2024/8dz5_27789.pdb" } resolution = 3.84 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= -0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5655 2.51 5 N 1530 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ASP 97": "OD1" <-> "OD2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 280 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 10, 'TRANS': 29} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "D" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "F" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 5.23, per 1000 atoms: 0.58 Number of scatterers: 8950 At special positions: 0 Unit cell: (72.45, 112.7, 115, 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 35 16.00 O 1730 8.00 N 1530 7.00 C 5655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 31 sheets defined 8.5% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.520A pdb=" N GLN H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.699A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.701A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.594A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.601A pdb=" N GLN C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.565A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.532A pdb=" N GLN E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.773A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.556A pdb=" N GLN M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' 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 'H' and resid 3 through 7 removed outlier: 3.547A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.389A pdb=" N GLY H 10 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.389A pdb=" N GLY H 10 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS H 92 " --> pdb=" O TRP H 102 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TRP H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS H 94 " --> pdb=" O ASP H 100C" (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.703A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 33 through 35 removed outlier: 4.151A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.916A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.275A pdb=" N GLY A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.275A pdb=" N GLY A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS A 92 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP A 102 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 94 " --> pdb=" O ASP A 100C" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.805A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.554A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 89 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.732A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 70 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.788A pdb=" N ALA C 93 " --> pdb=" O HIS C 35 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.785A pdb=" N CYS C 92 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS C 94 " --> pdb=" O ASP C 100C" (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.535A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.432A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 37 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.937A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.509A pdb=" N ALA E 93 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.591A pdb=" N CYS E 92 " --> pdb=" O TRP E 102 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 102 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS E 94 " --> pdb=" O ASP E 100C" (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.481A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN F 89 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.776A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.492A pdb=" N GLY M 10 " --> pdb=" O THR M 109 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.492A pdb=" N GLY M 10 " --> pdb=" O THR M 109 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS M 92 " --> pdb=" O TRP M 102 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP M 102 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS M 94 " --> pdb=" O ASP M 100C" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.506A pdb=" N GLN N 37 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU N 47 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 750 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: 2.53 Time building geometry restraints manager: 3.66 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: 2879 1.34 - 1.46: 2279 1.46 - 1.58: 3956 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 9164 Sorted by residual: bond pdb=" N GLY F 64 " pdb=" CA GLY F 64 " ideal model delta sigma weight residual 1.454 1.443 0.012 9.90e-03 1.02e+04 1.35e+00 bond pdb=" CA ASP C 100C" pdb=" C ASP C 100C" ideal model delta sigma weight residual 1.521 1.532 -0.011 9.90e-03 1.02e+04 1.35e+00 bond pdb=" CB ASP H 100C" pdb=" CG ASP H 100C" ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB PRO I 50 " pdb=" CG PRO I 50 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" CB GLU N 81 " pdb=" CG GLU N 81 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.62e-01 ... (remaining 9159 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.79: 189 105.79 - 112.85: 4704 112.85 - 119.91: 2986 119.91 - 126.96: 4419 126.96 - 134.02: 129 Bond angle restraints: 12427 Sorted by residual: angle pdb=" CA GLU N 105 " pdb=" CB GLU N 105 " pdb=" CG GLU N 105 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA GLU N 81 " pdb=" CB GLU N 81 " pdb=" CG GLU N 81 " ideal model delta sigma weight residual 114.10 119.55 -5.45 2.00e+00 2.50e-01 7.44e+00 angle pdb=" N ILE F 29 " pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 111.64 109.47 2.17 8.20e-01 1.49e+00 7.02e+00 angle pdb=" N LYS D 50 " pdb=" CA LYS D 50 " pdb=" C LYS D 50 " ideal model delta sigma weight residual 112.86 109.71 3.15 1.22e+00 6.72e-01 6.68e+00 angle pdb=" C ASP F 17 " pdb=" CA ASP F 17 " pdb=" CB ASP F 17 " ideal model delta sigma weight residual 109.76 114.84 -5.08 1.99e+00 2.53e-01 6.53e+00 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4789 17.78 - 35.56: 459 35.56 - 53.34: 98 53.34 - 71.11: 26 71.11 - 88.89: 12 Dihedral angle restraints: 5384 sinusoidal: 2100 harmonic: 3284 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual -86.00 -128.94 42.94 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual -86.00 -126.77 40.77 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual -86.00 -123.86 37.86 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 5381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 823 0.029 - 0.059: 332 0.059 - 0.088: 81 0.088 - 0.117: 77 0.117 - 0.147: 22 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ASP C 100C" pdb=" N ASP C 100C" pdb=" C ASP C 100C" pdb=" CB ASP C 100C" both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CG LEU D 33 " pdb=" CB LEU D 33 " pdb=" CD1 LEU D 33 " pdb=" CD2 LEU D 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1332 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 40 " -0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO A 41 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 91 " 0.016 2.00e-02 2.50e+03 1.29e-02 3.33e+00 pdb=" CG TYR N 91 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR N 91 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR N 91 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR N 91 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 91 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR N 91 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 91 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 39 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO B 40 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " 0.021 5.00e-02 4.00e+02 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 431 2.71 - 3.26: 8584 3.26 - 3.81: 14663 3.81 - 4.35: 17872 4.35 - 4.90: 30731 Nonbonded interactions: 72281 Sorted by model distance: nonbonded pdb=" OD1 ASP C 100C" pdb=" N TYR C 101 " model vdw 2.167 2.520 nonbonded pdb=" O TYR H 32 " pdb=" NH1 ARG H 71 " model vdw 2.221 2.520 nonbonded pdb=" O TYR C 32 " pdb=" NH1 ARG C 71 " model vdw 2.231 2.520 nonbonded pdb=" ND2 ASN I 43 " pdb=" O TYR L 91 " model vdw 2.246 2.520 nonbonded pdb=" OG1 THR E 28 " pdb=" OD2 ASP N 1 " model vdw 2.247 2.440 ... (remaining 72276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.800 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.310 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9164 Z= 0.189 Angle : 0.713 7.497 12427 Z= 0.399 Chirality : 0.042 0.147 1335 Planarity : 0.004 0.081 1594 Dihedral : 15.288 88.892 3274 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.62 % Allowed : 18.34 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -0.97 (0.23), residues: 495 loop : 0.25 (0.28), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 102 HIS 0.005 0.002 HIS M 35 PHE 0.016 0.002 PHE A 79 TYR 0.028 0.002 TYR N 91 ARG 0.011 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7476 (ptpp) REVERT: A 80 LEU cc_start: 0.7136 (tt) cc_final: 0.6845 (tt) outliers start: 6 outliers final: 5 residues processed: 138 average time/residue: 0.2717 time to fit residues: 49.0160 Evaluate side-chains 122 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN M 3 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 HIS N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9164 Z= 0.476 Angle : 0.694 7.328 12427 Z= 0.372 Chirality : 0.045 0.151 1335 Planarity : 0.005 0.051 1594 Dihedral : 5.880 51.286 1263 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 6.11 % Allowed : 15.75 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.24 (0.22), residues: 545 loop : -0.17 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 102 HIS 0.006 0.002 HIS M 96 PHE 0.017 0.002 PHE A 79 TYR 0.021 0.003 TYR E 90 ARG 0.005 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7089 (ttt-90) REVERT: A 67 PHE cc_start: 0.7469 (m-10) cc_final: 0.6568 (m-10) REVERT: A 100 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.4260 (mp10) REVERT: B 103 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7997 (tttt) REVERT: C 45 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7442 (mt) REVERT: C 53 ASP cc_start: 0.7488 (p0) cc_final: 0.7253 (p0) REVERT: C 100 ASP cc_start: 0.8233 (p0) cc_final: 0.7879 (p0) REVERT: C 102 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8581 (m100) REVERT: N 58 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7949 (p) REVERT: N 105 GLU cc_start: 0.7177 (tp30) cc_final: 0.6473 (tm-30) outliers start: 59 outliers final: 39 residues processed: 165 average time/residue: 0.2353 time to fit residues: 52.4856 Evaluate side-chains 159 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 1 ASP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 73 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9164 Z= 0.301 Angle : 0.615 7.140 12427 Z= 0.328 Chirality : 0.044 0.143 1335 Planarity : 0.004 0.041 1594 Dihedral : 5.748 58.348 1261 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.56 % Allowed : 18.03 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.08 (0.22), residues: 525 loop : -0.27 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 102 HIS 0.005 0.001 HIS A 35 PHE 0.013 0.002 PHE A 79 TYR 0.017 0.002 TYR E 101 ARG 0.004 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8800 (pttt) cc_final: 0.8437 (pttm) REVERT: B 17 ASP cc_start: 0.7309 (t0) cc_final: 0.6452 (m-30) REVERT: B 87 TYR cc_start: 0.7936 (m-80) cc_final: 0.7723 (m-10) REVERT: B 103 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7866 (tttt) REVERT: C 45 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7306 (mt) REVERT: C 53 ASP cc_start: 0.7507 (p0) cc_final: 0.7184 (p0) REVERT: C 100 ASP cc_start: 0.8143 (p0) cc_final: 0.7760 (p0) REVERT: C 102 TRP cc_start: 0.8865 (OUTLIER) cc_final: 0.8659 (m100) REVERT: N 105 GLU cc_start: 0.7166 (tp30) cc_final: 0.6486 (tm-30) outliers start: 44 outliers final: 33 residues processed: 148 average time/residue: 0.2431 time to fit residues: 48.0186 Evaluate side-chains 148 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 1 ASP Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9164 Z= 0.277 Angle : 0.598 7.339 12427 Z= 0.316 Chirality : 0.043 0.140 1335 Planarity : 0.004 0.036 1594 Dihedral : 5.775 58.086 1261 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.80 % Allowed : 16.99 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.09 (0.22), residues: 525 loop : -0.23 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 102 HIS 0.004 0.001 HIS A 35 PHE 0.010 0.002 PHE E 52A TYR 0.014 0.002 TYR E 101 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8781 (pttt) cc_final: 0.8415 (pttm) REVERT: B 17 ASP cc_start: 0.7496 (t0) cc_final: 0.6496 (m-30) REVERT: B 103 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7932 (tttt) REVERT: C 45 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7360 (mt) REVERT: C 53 ASP cc_start: 0.7500 (p0) cc_final: 0.7173 (p0) REVERT: C 100 ASP cc_start: 0.8143 (p0) cc_final: 0.7770 (p0) REVERT: C 102 TRP cc_start: 0.8853 (OUTLIER) cc_final: 0.8611 (m100) REVERT: F 49 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.8150 (p90) REVERT: M 82 MET cc_start: 0.7878 (mtt) cc_final: 0.7660 (mtt) REVERT: N 105 GLU cc_start: 0.7154 (tp30) cc_final: 0.6556 (tm-30) outliers start: 56 outliers final: 43 residues processed: 161 average time/residue: 0.2506 time to fit residues: 53.5760 Evaluate side-chains 155 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 1 ASP Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9164 Z= 0.286 Angle : 0.605 7.876 12427 Z= 0.318 Chirality : 0.043 0.143 1335 Planarity : 0.004 0.031 1594 Dihedral : 5.527 57.871 1259 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 6.11 % Allowed : 17.51 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.13 (0.22), residues: 535 loop : -0.12 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 102 HIS 0.004 0.001 HIS A 35 PHE 0.010 0.001 PHE A 79 TYR 0.012 0.002 TYR E 101 ARG 0.006 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 119 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8799 (pttt) cc_final: 0.8409 (pttm) REVERT: A 67 PHE cc_start: 0.7562 (m-10) cc_final: 0.6713 (m-10) REVERT: A 82 MET cc_start: 0.6941 (mmm) cc_final: 0.6592 (mmt) REVERT: B 17 ASP cc_start: 0.7287 (t0) cc_final: 0.6224 (m-30) REVERT: B 24 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7467 (ttm-80) REVERT: C 45 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7338 (mt) REVERT: C 53 ASP cc_start: 0.7466 (p0) cc_final: 0.7117 (p0) REVERT: C 100 ASP cc_start: 0.8222 (p0) cc_final: 0.7695 (p0) REVERT: C 102 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.8593 (m100) REVERT: E 53 ASP cc_start: 0.8255 (p0) cc_final: 0.7629 (p0) REVERT: E 82 MET cc_start: 0.8574 (tpp) cc_final: 0.8264 (mmt) REVERT: E 100 ASP cc_start: 0.7758 (p0) cc_final: 0.7468 (t0) REVERT: F 49 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8170 (p90) REVERT: M 82 MET cc_start: 0.7943 (mtt) cc_final: 0.7728 (mtt) REVERT: M 82 SER cc_start: 0.9311 (m) cc_final: 0.9089 (p) REVERT: N 105 GLU cc_start: 0.7076 (tp30) cc_final: 0.6731 (tm-30) outliers start: 59 outliers final: 50 residues processed: 164 average time/residue: 0.2525 time to fit residues: 55.0121 Evaluate side-chains 164 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 111 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 1 ASP Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 73 ASN N 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9164 Z= 0.156 Angle : 0.577 9.506 12427 Z= 0.295 Chirality : 0.042 0.138 1335 Planarity : 0.003 0.029 1594 Dihedral : 5.044 54.929 1259 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.56 % Allowed : 19.07 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -1.07 (0.22), residues: 545 loop : 0.12 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 102 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE E 52A TYR 0.015 0.001 TYR H 90 ARG 0.007 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8740 (pttt) cc_final: 0.8359 (pttm) REVERT: A 57 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7519 (ptmt) REVERT: A 67 PHE cc_start: 0.7471 (m-10) cc_final: 0.6640 (m-10) REVERT: A 82 MET cc_start: 0.6809 (mmm) cc_final: 0.6525 (mmt) REVERT: B 17 ASP cc_start: 0.7290 (t0) cc_final: 0.6218 (m-30) REVERT: B 18 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7936 (ttp80) REVERT: B 100 GLN cc_start: 0.8106 (pt0) cc_final: 0.7874 (mt0) REVERT: B 105 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7614 (tm-30) REVERT: C 45 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7153 (mt) REVERT: C 53 ASP cc_start: 0.7322 (p0) cc_final: 0.6989 (p0) REVERT: C 100 ASP cc_start: 0.8209 (p0) cc_final: 0.7825 (p0) REVERT: E 53 ASP cc_start: 0.8214 (p0) cc_final: 0.7572 (p0) REVERT: E 82 MET cc_start: 0.8505 (tpp) cc_final: 0.8149 (mmt) REVERT: M 82 SER cc_start: 0.9321 (m) cc_final: 0.9093 (p) REVERT: N 105 GLU cc_start: 0.7145 (tp30) cc_final: 0.6727 (tm-30) outliers start: 44 outliers final: 28 residues processed: 160 average time/residue: 0.2405 time to fit residues: 51.2901 Evaluate side-chains 141 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN M 3 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9164 Z= 0.281 Angle : 0.617 8.291 12427 Z= 0.319 Chirality : 0.043 0.145 1335 Planarity : 0.004 0.035 1594 Dihedral : 5.036 52.942 1257 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.08 % Allowed : 19.48 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -1.09 (0.22), residues: 545 loop : 0.08 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.004 0.001 HIS A 35 PHE 0.009 0.001 PHE A 79 TYR 0.020 0.002 TYR B 91 ARG 0.013 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8784 (pttt) cc_final: 0.8387 (pttm) REVERT: A 57 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7543 (ptmt) REVERT: A 67 PHE cc_start: 0.7552 (m-10) cc_final: 0.6672 (m-10) REVERT: A 82 MET cc_start: 0.6819 (mmm) cc_final: 0.6514 (mmt) REVERT: B 17 ASP cc_start: 0.7453 (t0) cc_final: 0.6477 (m-30) REVERT: B 24 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: B 46 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8244 (tt) REVERT: C 45 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7245 (mt) REVERT: C 53 ASP cc_start: 0.7339 (p0) cc_final: 0.7030 (p0) REVERT: C 100 ASP cc_start: 0.8035 (p0) cc_final: 0.7700 (p0) REVERT: E 53 ASP cc_start: 0.8253 (p0) cc_final: 0.7598 (p0) REVERT: E 82 MET cc_start: 0.8461 (tpp) cc_final: 0.8095 (mmt) REVERT: N 105 GLU cc_start: 0.7206 (tp30) cc_final: 0.6714 (tm-30) outliers start: 49 outliers final: 40 residues processed: 152 average time/residue: 0.2473 time to fit residues: 50.0244 Evaluate side-chains 153 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN M 3 GLN M 73 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9164 Z= 0.282 Angle : 0.620 8.498 12427 Z= 0.320 Chirality : 0.043 0.174 1335 Planarity : 0.004 0.038 1594 Dihedral : 5.091 52.843 1257 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.49 % Allowed : 19.17 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.09 (0.22), residues: 545 loop : 0.04 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.005 0.001 HIS A 35 PHE 0.009 0.001 PHE A 79 TYR 0.017 0.002 TYR H 90 ARG 0.010 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 116 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8793 (pttt) cc_final: 0.8395 (pttm) REVERT: A 57 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7481 (ptmt) REVERT: A 67 PHE cc_start: 0.7648 (m-10) cc_final: 0.6702 (m-10) REVERT: B 17 ASP cc_start: 0.7436 (t0) cc_final: 0.6573 (m-30) REVERT: B 24 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7246 (ttm-80) REVERT: B 46 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 105 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7593 (tm-30) REVERT: C 45 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7548 (mt) REVERT: C 53 ASP cc_start: 0.7386 (p0) cc_final: 0.7075 (p0) REVERT: C 100 ASP cc_start: 0.8032 (p0) cc_final: 0.7767 (p0) REVERT: E 53 ASP cc_start: 0.8293 (p0) cc_final: 0.7940 (p0) REVERT: E 82 MET cc_start: 0.8402 (tpp) cc_final: 0.8069 (mmt) REVERT: N 105 GLU cc_start: 0.7199 (tp30) cc_final: 0.6685 (tm-30) outliers start: 53 outliers final: 42 residues processed: 160 average time/residue: 0.2634 time to fit residues: 57.3833 Evaluate side-chains 155 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 110 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN D 90 GLN M 3 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9164 Z= 0.482 Angle : 0.714 9.331 12427 Z= 0.371 Chirality : 0.045 0.150 1335 Planarity : 0.005 0.045 1594 Dihedral : 5.671 49.549 1257 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 6.32 % Allowed : 19.07 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.31 (0.22), residues: 545 loop : -0.25 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 35 HIS 0.007 0.002 HIS A 35 PHE 0.015 0.002 PHE F 62 TYR 0.020 0.003 TYR M 91 ARG 0.010 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 108 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8874 (pttt) cc_final: 0.8407 (pttm) REVERT: A 57 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7452 (ptmt) REVERT: B 17 ASP cc_start: 0.7745 (t0) cc_final: 0.6791 (m-30) REVERT: B 24 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: B 46 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8173 (tt) REVERT: B 105 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7606 (tm-30) REVERT: C 45 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7816 (mt) REVERT: C 53 ASP cc_start: 0.7492 (p0) cc_final: 0.7194 (p0) REVERT: C 100 ASP cc_start: 0.8103 (p0) cc_final: 0.7878 (p0) REVERT: D 49 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7889 (p90) REVERT: E 53 ASP cc_start: 0.8334 (p0) cc_final: 0.7985 (p0) REVERT: E 82 MET cc_start: 0.8495 (tpp) cc_final: 0.8115 (mmt) outliers start: 61 outliers final: 51 residues processed: 157 average time/residue: 0.2610 time to fit residues: 55.2180 Evaluate side-chains 160 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 105 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 1 ASP Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9164 Z= 0.188 Angle : 0.648 10.345 12427 Z= 0.329 Chirality : 0.043 0.156 1335 Planarity : 0.004 0.039 1594 Dihedral : 5.109 50.191 1257 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.94 % Allowed : 21.66 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.14 (0.22), residues: 545 loop : 0.05 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 102 HIS 0.003 0.001 HIS A 35 PHE 0.015 0.001 PHE A 67 TYR 0.028 0.001 TYR B 91 ARG 0.009 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8773 (pttt) cc_final: 0.8383 (pttm) REVERT: A 57 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7383 (ptmt) REVERT: B 17 ASP cc_start: 0.7685 (t0) cc_final: 0.6738 (m-30) REVERT: B 24 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7383 (ttm-80) REVERT: C 45 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7637 (mt) REVERT: C 53 ASP cc_start: 0.7395 (p0) cc_final: 0.7070 (p0) REVERT: E 53 ASP cc_start: 0.8292 (p0) cc_final: 0.7911 (p0) REVERT: E 82 MET cc_start: 0.8414 (tpp) cc_final: 0.8024 (mmt) REVERT: N 105 GLU cc_start: 0.7168 (tp30) cc_final: 0.6751 (tm-30) outliers start: 38 outliers final: 31 residues processed: 145 average time/residue: 0.2482 time to fit residues: 47.6962 Evaluate side-chains 144 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067217 restraints weight = 22102.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069484 restraints weight = 13920.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071060 restraints weight = 10109.328| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9164 Z= 0.351 Angle : 0.671 8.676 12427 Z= 0.347 Chirality : 0.044 0.190 1335 Planarity : 0.004 0.041 1594 Dihedral : 5.355 49.010 1257 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.35 % Allowed : 20.93 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -1.25 (0.22), residues: 545 loop : -0.06 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.005 0.001 HIS A 35 PHE 0.013 0.002 PHE A 79 TYR 0.018 0.002 TYR H 90 ARG 0.009 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.85 seconds wall clock time: 35 minutes 1.25 seconds (2101.25 seconds total)