Starting phenix.real_space_refine on Tue Feb 13 22:46:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbz_27318/02_2024/8dbz_27318.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbz_27318/02_2024/8dbz_27318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbz_27318/02_2024/8dbz_27318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbz_27318/02_2024/8dbz_27318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbz_27318/02_2024/8dbz_27318.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbz_27318/02_2024/8dbz_27318.pdb" } resolution = 4.1 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= 0.000 sd= 1.000 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 32 5.16 5 C 4956 2.51 5 N 1409 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7960 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 273} Chain breaks: 3 Chain: "D" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "C" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 507 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 93} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 531 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 173 Chain: "H" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 507 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 93} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "I" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 531 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 173 Time building chain proxies: 5.15, per 1000 atoms: 0.65 Number of scatterers: 7960 At special positions: 0 Unit cell: (100.74, 129.94, 135.78, 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 32 16.00 O 1563 8.00 N 1409 7.00 C 4956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 93 " 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: 2.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 29 sheets defined 9.0% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.362A pdb=" N MET A 73 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.719A pdb=" N TYR A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 124 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.813A pdb=" N MET A 156 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.863A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.825A pdb=" N ASN B 30 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 76 through 82 removed outlier: 3.867A pdb=" N HIS G 82 " --> pdb=" O ASP G 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 4.356A pdb=" N GLY H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 77' Processing helix chain 'I' and resid 14 through 19 Processing helix chain 'I' and resid 76 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.438A pdb=" N TYR A 24 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE A 173 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 26 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 165 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.535A pdb=" N VAL A 146 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 45 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 105 removed outlier: 3.852A pdb=" N LYS A 105 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 80 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.044A pdb=" N LEU A 259 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 250 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 301 removed outlier: 6.460A pdb=" N ALA A 318 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 316 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.959A pdb=" N THR D 122 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.347A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 21 through 22 removed outlier: 4.695A pdb=" N LEU E 21 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 74 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.045A pdb=" N THR B 121 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.659A pdb=" N ILE C 21 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 68 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 50 through 53 removed outlier: 3.663A pdb=" N LEU C 52 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP C 40 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 7 through 11 removed outlier: 3.883A pdb=" N SER F 7 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE F 9 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 7 through 11 removed outlier: 3.883A pdb=" N SER F 7 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE F 9 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 67 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.398A pdb=" N THR F 38 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 86 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL F 85 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 94 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR F 92 " --> pdb=" O HIS F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.536A pdb=" N VAL F 56 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.647A pdb=" N PHE G 9 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU G 28 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER G 70 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN G 30 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU G 68 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 55 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.534A pdb=" N LEU G 74 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.597A pdb=" N CYS G 87 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 100 " --> pdb=" O CYS G 87 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 89 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 7 through 11 removed outlier: 3.653A pdb=" N LEU H 25 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL H 69 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS H 27 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H 67 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR H 63 " --> pdb=" O ASP H 31 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS H 51 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.653A pdb=" N LEU H 25 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL H 69 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS H 27 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H 67 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR H 63 " --> pdb=" O ASP H 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 41 Processing sheet with id=AD1, first strand: chain 'I' and resid 7 through 11 removed outlier: 3.825A pdb=" N SER I 7 " --> pdb=" O ASN I 30 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN I 30 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE I 9 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 26 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER I 70 " --> pdb=" O CYS I 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 68 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN I 31 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR I 66 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER I 55 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 38 through 43 removed outlier: 3.533A pdb=" N LYS I 38 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL I 89 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 98 " --> pdb=" O VAL I 89 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 627 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: 2.36 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2721 1.35 - 1.47: 1887 1.47 - 1.59: 3435 1.59 - 1.71: 0 1.71 - 1.83: 44 Bond restraints: 8087 Sorted by residual: bond pdb=" CA GLU E 17 " pdb=" CB GLU E 17 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.68e+00 bond pdb=" CA ASP E 83 " pdb=" CB ASP E 83 " ideal model delta sigma weight residual 1.524 1.543 -0.020 1.62e-02 3.81e+03 1.48e+00 bond pdb=" N PHE F 9 " pdb=" CA PHE F 9 " ideal model delta sigma weight residual 1.463 1.448 0.015 1.22e-02 6.72e+03 1.41e+00 bond pdb=" CG1 ILE D 52 " pdb=" CD1 ILE D 52 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.27e+00 bond pdb=" CB TRP B 36 " pdb=" CG TRP B 36 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.24e+00 ... (remaining 8082 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 189 106.10 - 113.09: 4415 113.09 - 120.08: 2491 120.08 - 127.07: 3878 127.07 - 134.06: 77 Bond angle restraints: 11050 Sorted by residual: angle pdb=" N LEU C 52 " pdb=" CA LEU C 52 " pdb=" C LEU C 52 " ideal model delta sigma weight residual 114.39 108.42 5.97 1.45e+00 4.76e-01 1.69e+01 angle pdb=" C GLU E 69 " pdb=" CA GLU E 69 " pdb=" CB GLU E 69 " ideal model delta sigma weight residual 115.89 110.59 5.30 1.32e+00 5.74e-01 1.61e+01 angle pdb=" CA GLU E 17 " pdb=" CB GLU E 17 " pdb=" CG GLU E 17 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA GLY E 103 " pdb=" C GLY E 103 " pdb=" O GLY E 103 " ideal model delta sigma weight residual 122.23 120.00 2.23 6.90e-01 2.10e+00 1.04e+01 angle pdb=" CA ARG A 268 " pdb=" CB ARG A 268 " pdb=" CG ARG A 268 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.75e+00 ... (remaining 11045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 4390 16.38 - 32.75: 338 32.75 - 49.13: 59 49.13 - 65.50: 15 65.50 - 81.88: 8 Dihedral angle restraints: 4810 sinusoidal: 1411 harmonic: 3399 Sorted by residual: dihedral pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -139.98 53.98 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 132 " pdb=" CB CYS A 132 " ideal model delta sinusoidal sigma weight residual -86.00 -34.15 -51.85 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CA TYR E 92 " pdb=" C TYR E 92 " pdb=" N GLY E 93 " pdb=" CA GLY E 93 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 4807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 904 0.039 - 0.077: 268 0.077 - 0.116: 124 0.116 - 0.155: 21 0.155 - 0.193: 5 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA PRO B 53 " pdb=" N PRO B 53 " pdb=" C PRO B 53 " pdb=" CB PRO B 53 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA ILE B 52 " pdb=" N ILE B 52 " pdb=" C ILE B 52 " pdb=" CB ILE B 52 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1319 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 72 " 0.010 2.00e-02 2.50e+03 1.86e-02 6.08e+00 pdb=" CG PHE E 72 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE E 72 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 72 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 72 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE E 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 261 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 262 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 80 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO E 81 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.030 5.00e-02 4.00e+02 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 183 2.66 - 3.22: 7606 3.22 - 3.78: 11858 3.78 - 4.34: 15349 4.34 - 4.90: 24485 Nonbonded interactions: 59481 Sorted by model distance: nonbonded pdb=" OG SER E 22 " pdb=" OG1 THR E 73 " model vdw 2.101 2.440 nonbonded pdb=" ND2 ASN A 334 " pdb=" OE2 GLU A 338 " model vdw 2.108 2.520 nonbonded pdb=" O ARG A 333 " pdb=" NH1 ARG A 333 " model vdw 2.128 2.520 nonbonded pdb=" O SER A 263 " pdb=" NH2 ARG B 102 " model vdw 2.183 2.520 nonbonded pdb=" OH TYR A 248 " pdb=" O PRO A 360 " model vdw 2.216 2.440 ... (remaining 59476 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 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 0.400 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: 1.720 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 25.570 Find NCS groups from input model: 0.380 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 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 0.044 8087 Z= 0.225 Angle : 0.732 8.438 11050 Z= 0.408 Chirality : 0.046 0.193 1322 Planarity : 0.005 0.060 1455 Dihedral : 12.606 81.876 2590 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.42 (0.25), residues: 1160 helix: -0.47 (0.69), residues: 55 sheet: -0.64 (0.26), residues: 421 loop : -1.17 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 117 HIS 0.003 0.001 HIS A 351 PHE 0.037 0.002 PHE E 72 TYR 0.036 0.002 TYR E 92 ARG 0.007 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8133 (tpp) cc_final: 0.7327 (tpp) REVERT: A 363 TRP cc_start: 0.4346 (t60) cc_final: 0.3742 (t60) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2188 time to fit residues: 37.4859 Evaluate side-chains 97 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS D 65 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8087 Z= 0.245 Angle : 0.647 8.316 11050 Z= 0.346 Chirality : 0.046 0.200 1322 Planarity : 0.005 0.072 1455 Dihedral : 5.662 47.596 1248 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 0.30 % Allowed : 6.08 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.34 (0.26), residues: 1160 helix: -0.10 (0.71), residues: 55 sheet: -0.59 (0.24), residues: 461 loop : -1.15 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 36 HIS 0.005 0.001 HIS A 351 PHE 0.023 0.002 PHE E 72 TYR 0.024 0.002 TYR C 41 ARG 0.007 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.6684 (tm-30) cc_final: 0.5998 (tt0) REVERT: A 308 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.6839 (m) REVERT: A 356 LYS cc_start: 0.7680 (mttm) cc_final: 0.7298 (ttmm) REVERT: D 38 ARG cc_start: 0.7466 (ttp-170) cc_final: 0.7221 (ttm-80) REVERT: D 106 TYR cc_start: 0.4972 (t80) cc_final: 0.2704 (t80) REVERT: E 32 ARG cc_start: 0.4790 (tpt170) cc_final: 0.4557 (tpm170) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1869 time to fit residues: 32.9161 Evaluate side-chains 97 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8087 Z= 0.343 Angle : 0.716 8.450 11050 Z= 0.380 Chirality : 0.048 0.213 1322 Planarity : 0.005 0.054 1455 Dihedral : 6.011 37.985 1248 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.88 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.67 (0.25), residues: 1160 helix: -0.41 (0.69), residues: 58 sheet: -0.79 (0.25), residues: 447 loop : -1.38 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP B 36 HIS 0.004 0.001 HIS A 351 PHE 0.018 0.003 PHE C 99 TYR 0.025 0.003 TYR D 111 ARG 0.005 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.6763 (tm-30) cc_final: 0.5761 (tp30) REVERT: A 356 LYS cc_start: 0.7826 (mttm) cc_final: 0.7372 (ttmm) REVERT: D 106 TYR cc_start: 0.5348 (t80) cc_final: 0.3379 (t80) REVERT: E 32 ARG cc_start: 0.5807 (tpt170) cc_final: 0.5304 (tpm170) REVERT: B 80 TYR cc_start: 0.8463 (m-80) cc_final: 0.8078 (m-80) REVERT: B 112 TYR cc_start: 0.7779 (p90) cc_final: 0.7539 (p90) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2105 time to fit residues: 34.5656 Evaluate side-chains 98 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 20.0000 chunk 77 optimal weight: 0.0070 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8087 Z= 0.191 Angle : 0.613 9.406 11050 Z= 0.323 Chirality : 0.046 0.184 1322 Planarity : 0.005 0.068 1455 Dihedral : 5.443 38.156 1248 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 0.15 % Allowed : 5.17 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.41 (0.26), residues: 1160 helix: 0.11 (0.71), residues: 58 sheet: -0.65 (0.25), residues: 453 loop : -1.22 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 36 HIS 0.003 0.001 HIS A 69 PHE 0.016 0.002 PHE B 106 TYR 0.028 0.002 TYR E 92 ARG 0.006 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.6814 (tm-30) cc_final: 0.5758 (tp30) REVERT: A 356 LYS cc_start: 0.7683 (mttm) cc_final: 0.7295 (ttmm) REVERT: A 363 TRP cc_start: 0.3840 (t60) cc_final: 0.3357 (t60) REVERT: D 46 GLU cc_start: 0.5053 (pt0) cc_final: 0.4074 (mm-30) REVERT: D 106 TYR cc_start: 0.4965 (t80) cc_final: 0.2746 (t80) REVERT: E 32 ARG cc_start: 0.4920 (tpt170) cc_final: 0.4306 (tpm170) REVERT: B 80 TYR cc_start: 0.8175 (m-80) cc_final: 0.7660 (m-80) REVERT: B 105 TYR cc_start: 0.6332 (t80) cc_final: 0.5003 (t80) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1815 time to fit residues: 34.4363 Evaluate side-chains 108 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 40.0000 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8087 Z= 0.304 Angle : 0.687 8.105 11050 Z= 0.361 Chirality : 0.048 0.207 1322 Planarity : 0.005 0.074 1455 Dihedral : 5.751 38.865 1248 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.25), residues: 1160 helix: 0.10 (0.72), residues: 58 sheet: -0.78 (0.24), residues: 461 loop : -1.31 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 36 HIS 0.005 0.001 HIS B 104 PHE 0.019 0.002 PHE C 76 TYR 0.032 0.003 TYR E 92 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 TYR cc_start: 0.5246 (t80) cc_final: 0.3345 (t80) REVERT: B 80 TYR cc_start: 0.8324 (m-80) cc_final: 0.7942 (m-80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1809 time to fit residues: 31.9263 Evaluate side-chains 101 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8087 Z= 0.325 Angle : 0.706 7.884 11050 Z= 0.373 Chirality : 0.048 0.214 1322 Planarity : 0.005 0.065 1455 Dihedral : 5.899 39.104 1248 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1160 helix: -0.07 (0.72), residues: 58 sheet: -0.83 (0.24), residues: 454 loop : -1.34 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP E 36 HIS 0.003 0.001 HIS A 351 PHE 0.025 0.003 PHE E 72 TYR 0.022 0.003 TYR E 92 ARG 0.004 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.7809 (m) cc_final: 0.7511 (p) REVERT: A 363 TRP cc_start: 0.4497 (t60) cc_final: 0.3876 (t60) REVERT: D 106 TYR cc_start: 0.5353 (t80) cc_final: 0.3198 (t80) REVERT: E 32 ARG cc_start: 0.4739 (tpt170) cc_final: 0.3590 (tpp-160) REVERT: B 80 TYR cc_start: 0.8311 (m-80) cc_final: 0.7909 (m-80) REVERT: C 4 MET cc_start: 0.8096 (ppp) cc_final: 0.7887 (ppp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1992 time to fit residues: 34.4217 Evaluate side-chains 101 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 40.0000 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 223 GLN D 65 HIS D 102 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8087 Z= 0.184 Angle : 0.617 8.172 11050 Z= 0.321 Chirality : 0.045 0.178 1322 Planarity : 0.005 0.072 1455 Dihedral : 5.343 35.980 1248 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1160 helix: 0.15 (0.71), residues: 60 sheet: -0.46 (0.25), residues: 442 loop : -1.18 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP E 36 HIS 0.003 0.001 HIS B 104 PHE 0.028 0.002 PHE E 72 TYR 0.025 0.002 TYR E 92 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7765 (tpp) cc_final: 0.7040 (tpp) REVERT: A 363 TRP cc_start: 0.4027 (t60) cc_final: 0.3579 (t60) REVERT: D 10 GLU cc_start: 0.5178 (pm20) cc_final: 0.4604 (mm-30) REVERT: D 46 GLU cc_start: 0.4723 (pt0) cc_final: 0.3900 (mm-30) REVERT: D 106 TYR cc_start: 0.4731 (t80) cc_final: 0.2075 (t80) REVERT: D 121 VAL cc_start: 0.8452 (p) cc_final: 0.8246 (p) REVERT: E 32 ARG cc_start: 0.5157 (tpt170) cc_final: 0.3904 (tpp-160) REVERT: B 51 ILE cc_start: 0.7965 (tp) cc_final: 0.7608 (tp) REVERT: B 80 TYR cc_start: 0.8192 (m-80) cc_final: 0.7867 (m-80) REVERT: B 105 TYR cc_start: 0.6034 (t80) cc_final: 0.4800 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1937 time to fit residues: 36.4468 Evaluate side-chains 107 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8087 Z= 0.225 Angle : 0.637 7.969 11050 Z= 0.334 Chirality : 0.047 0.185 1322 Planarity : 0.005 0.077 1455 Dihedral : 5.423 35.326 1248 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1160 helix: 0.27 (0.72), residues: 60 sheet: -0.64 (0.25), residues: 454 loop : -1.16 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP E 36 HIS 0.004 0.001 HIS B 104 PHE 0.037 0.002 PHE E 72 TYR 0.020 0.002 TYR E 92 ARG 0.008 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7948 (tpp) cc_final: 0.7237 (tpp) REVERT: A 363 TRP cc_start: 0.3980 (t60) cc_final: 0.3444 (t60) REVERT: D 46 GLU cc_start: 0.4963 (pt0) cc_final: 0.4026 (mm-30) REVERT: D 106 TYR cc_start: 0.5177 (t80) cc_final: 0.2886 (t80) REVERT: D 120 LEU cc_start: 0.7558 (tp) cc_final: 0.7326 (tp) REVERT: E 32 ARG cc_start: 0.5977 (tpt170) cc_final: 0.4811 (tpp-160) REVERT: B 29 TYR cc_start: 0.1069 (m-80) cc_final: 0.0823 (m-80) REVERT: B 51 ILE cc_start: 0.8046 (tp) cc_final: 0.7781 (tp) REVERT: B 80 TYR cc_start: 0.8370 (m-80) cc_final: 0.7738 (m-80) REVERT: B 105 TYR cc_start: 0.6518 (t80) cc_final: 0.5074 (t80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1964 time to fit residues: 35.7027 Evaluate side-chains 102 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 8087 Z= 0.530 Angle : 0.870 9.719 11050 Z= 0.461 Chirality : 0.053 0.230 1322 Planarity : 0.006 0.058 1455 Dihedral : 6.609 43.099 1248 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 31.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.98 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 1160 helix: -0.31 (0.69), residues: 59 sheet: -0.92 (0.25), residues: 444 loop : -1.59 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP D 115 HIS 0.008 0.002 HIS B 104 PHE 0.040 0.004 PHE E 72 TYR 0.033 0.004 TYR B 105 ARG 0.009 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TRP cc_start: 0.4871 (t60) cc_final: 0.4336 (t60) REVERT: D 106 TYR cc_start: 0.6234 (t80) cc_final: 0.4180 (t80) REVERT: E 32 ARG cc_start: 0.6187 (tpt170) cc_final: 0.5235 (tpp-160) REVERT: E 92 TYR cc_start: 0.7057 (p90) cc_final: 0.6839 (p90) REVERT: B 29 TYR cc_start: 0.1574 (m-80) cc_final: 0.1227 (m-80) REVERT: B 80 TYR cc_start: 0.8563 (m-80) cc_final: 0.8003 (m-80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1880 time to fit residues: 31.3600 Evaluate side-chains 93 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8087 Z= 0.404 Angle : 0.799 9.631 11050 Z= 0.423 Chirality : 0.051 0.267 1322 Planarity : 0.006 0.080 1455 Dihedral : 6.435 42.101 1248 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 27.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.17 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.25), residues: 1160 helix: -0.35 (0.69), residues: 58 sheet: -1.02 (0.25), residues: 442 loop : -1.67 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 115 HIS 0.006 0.001 HIS B 104 PHE 0.054 0.003 PHE E 72 TYR 0.034 0.003 TYR E 92 ARG 0.007 0.001 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.6293 (tm-30) cc_final: 0.6060 (tm-30) REVERT: A 76 LYS cc_start: 0.8578 (mptt) cc_final: 0.8375 (mmtt) REVERT: A 231 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6308 (tt0) REVERT: A 363 TRP cc_start: 0.4525 (t60) cc_final: 0.3962 (t60) REVERT: D 46 GLU cc_start: 0.5655 (pt0) cc_final: 0.4981 (mm-30) REVERT: D 106 TYR cc_start: 0.5939 (t80) cc_final: 0.3508 (t80) REVERT: E 32 ARG cc_start: 0.6178 (tpt170) cc_final: 0.5244 (tpp-160) REVERT: E 92 TYR cc_start: 0.6817 (p90) cc_final: 0.6501 (p90) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1815 time to fit residues: 29.0052 Evaluate side-chains 91 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 30.0000 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.0170 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS D 102 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.193675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161032 restraints weight = 14383.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.163110 restraints weight = 11156.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.164566 restraints weight = 9240.347| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8087 Z= 0.244 Angle : 0.702 8.951 11050 Z= 0.367 Chirality : 0.048 0.247 1322 Planarity : 0.005 0.075 1455 Dihedral : 5.866 39.515 1248 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.28 % Favored : 91.64 % Rotamer: Outliers : 0.15 % Allowed : 0.61 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.26), residues: 1160 helix: 0.02 (0.71), residues: 59 sheet: -0.95 (0.25), residues: 454 loop : -1.43 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 104 HIS 0.003 0.001 HIS B 104 PHE 0.048 0.002 PHE E 72 TYR 0.034 0.003 TYR E 92 ARG 0.010 0.001 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.60 seconds wall clock time: 31 minutes 53.81 seconds (1913.81 seconds total)