Starting phenix.real_space_refine on Mon Mar 25 06:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/03_2024/6w6k_21558.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/03_2024/6w6k_21558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/03_2024/6w6k_21558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/03_2024/6w6k_21558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/03_2024/6w6k_21558.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/03_2024/6w6k_21558.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 1534 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 23419 2.51 5 N 8753 2.21 5 O 13183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 4": "OD1" <-> "OD2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J ASP 91": "OD1" <-> "OD2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "K PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "O PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 24": "OD1" <-> "OD2" Residue "R TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "S PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 72": "OE1" <-> "OE2" Residue "S PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 14": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46934 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 32917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32917 Classifications: {'RNA': 1534} Modifications used: {'rna2p_pur': 108, 'rna2p_pyr': 77, 'rna3p_pur': 767, 'rna3p_pyr': 582} Link IDs: {'rna2p': 185, 'rna3p': 1348} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 622 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 240 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 559 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 166 Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "P" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 629 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "T" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 659 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.45, per 1000 atoms: 0.52 Number of scatterers: 46934 At special positions: 0 Unit cell: (202.797, 218.892, 164.169, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 1534 15.00 Mg 1 11.99 O 13183 8.00 N 8753 7.00 C 23419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 24.07 Conformation dependent library (CDL) restraints added in 2.8 seconds 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 34.2% alpha, 11.0% beta 434 base pairs and 779 stacking pairs defined. Time for finding SS restraints: 22.02 Creating SS restraints... Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.673A pdb=" N LEU C 11 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 removed outlier: 4.108A pdb=" N LEU C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.003A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 77' Processing helix chain 'C' and resid 84 through 93 removed outlier: 4.014A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.573A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.901A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 14 removed outlier: 3.895A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 48 through 63 removed outlier: 3.630A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.611A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.562A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 157 through 164 removed outlier: 3.806A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.544A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 67 removed outlier: 3.617A pdb=" N ALA E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 117 removed outlier: 3.967A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 145 removed outlier: 3.501A pdb=" N ASN E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'H' and resid 5 through 15 removed outlier: 3.616A pdb=" N LEU H 10 " --> pdb=" O ILE H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 removed outlier: 3.521A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.807A pdb=" N LEU H 91 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 48 removed outlier: 4.025A pdb=" N VAL I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.808A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP I 90 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 3.942A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.701A pdb=" N LEU J 17 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 27 removed outlier: 3.512A pdb=" N VAL J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 22 through 27' Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.679A pdb=" N VAL K 64 " --> pdb=" O PHE K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 removed outlier: 3.638A pdb=" N ASP K 71 " --> pdb=" O ARG K 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 93 through 103 removed outlier: 3.827A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.922A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL L 7 " --> pdb=" O VAL L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 7' Processing helix chain 'M' and resid 13 through 20 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 48 through 58 removed outlier: 4.232A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 80 removed outlier: 3.575A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 2 through 19 removed outlier: 3.807A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 27 Processing helix chain 'N' and resid 41 through 47 removed outlier: 4.133A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.679A pdb=" N VAL N 83 " --> pdb=" O SER N 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.869A pdb=" N ALA O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 4.044A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.840A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.789A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.853A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 60 removed outlier: 4.134A pdb=" N ARG R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'S' and resid 11 through 22 removed outlier: 3.642A pdb=" N LEU S 15 " --> pdb=" O ASP S 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 69 through 73 removed outlier: 3.530A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 69 through 73' Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.575A pdb=" N GLN T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 63 Proline residue: T 55 - end of helix removed outlier: 3.579A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.696A pdb=" N HIS T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 5.933A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA5, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 17 removed outlier: 7.423A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL E 17 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR E 33 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 87 Processing sheet with id=AA8, first strand: chain 'F' and resid 63 through 64 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 27 removed outlier: 3.708A pdb=" N MET H 26 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'H' and resid 75 through 76 removed outlier: 3.798A pdb=" N GLU H 123 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.314A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 44 through 45 removed outlier: 3.997A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER J 101 " --> pdb=" O ARG J 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 48 through 49 removed outlier: 4.032A pdb=" N GLU J 66 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 40 through 43 removed outlier: 7.099A pdb=" N ILE K 33 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP K 43 " --> pdb=" O VAL K 31 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL K 31 " --> pdb=" O TRP K 43 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA K 20 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS K 86 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE K 22 " --> pdb=" O LYS K 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 51 through 55 Processing sheet with id=AB8, first strand: chain 'Q' and resid 7 through 9 removed outlier: 3.962A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG Q 61 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU Q 74 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS Q 63 " --> pdb=" O TRP Q 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP Q 72 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS Q 70 " --> pdb=" O PRO Q 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AC1, first strand: chain 'Q' and resid 25 through 29 removed outlier: 4.309A pdb=" N VAL Q 28 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE Q 37 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 47 through 51 removed outlier: 3.826A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1097 hydrogen bonds 1778 hydrogen bond angles 0 basepair planarities 434 basepair parallelities 779 stacking parallelities Total time for adding SS restraints: 45.97 Time building geometry restraints manager: 25.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8065 1.33 - 1.45: 20716 1.45 - 1.57: 19135 1.57 - 1.69: 3067 1.69 - 1.81: 77 Bond restraints: 51060 Sorted by residual: bond pdb=" N LEU J 92 " pdb=" CA LEU J 92 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.30e-02 5.92e+03 6.33e+00 bond pdb=" N LYS F 53 " pdb=" CA LYS F 53 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.23e+00 bond pdb=" N ASP J 91 " pdb=" CA ASP J 91 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.44e-02 4.82e+03 4.76e+00 bond pdb=" O5' G A 803 " pdb=" C5' G A 803 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.59e+00 bond pdb=" C THR L 39 " pdb=" N THR L 40 " ideal model delta sigma weight residual 1.331 1.377 -0.046 2.83e-02 1.25e+03 2.60e+00 ... (remaining 51055 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 9333 106.92 - 113.68: 31129 113.68 - 120.45: 18643 120.45 - 127.21: 14077 127.21 - 133.98: 3443 Bond angle restraints: 76625 Sorted by residual: angle pdb=" O3' G A 803 " pdb=" C3' G A 803 " pdb=" C2' G A 803 " ideal model delta sigma weight residual 113.70 107.49 6.21 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C3' U A1528 " pdb=" O3' U A1528 " pdb=" P G A1529 " ideal model delta sigma weight residual 120.20 125.77 -5.57 1.50e+00 4.44e-01 1.38e+01 angle pdb=" O3' U A1528 " pdb=" C3' U A1528 " pdb=" C2' U A1528 " ideal model delta sigma weight residual 109.50 115.02 -5.52 1.50e+00 4.44e-01 1.36e+01 angle pdb=" C3' A A1101 " pdb=" O3' A A1101 " pdb=" P A A1102 " ideal model delta sigma weight residual 120.20 125.60 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C3' U A1065 " pdb=" O3' U A1065 " pdb=" P C A1066 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 ... (remaining 76620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 28714 35.97 - 71.95: 3560 71.95 - 107.92: 422 107.92 - 143.90: 8 143.90 - 179.87: 10 Dihedral angle restraints: 32714 sinusoidal: 27362 harmonic: 5352 Sorted by residual: dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 41.70 158.30 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 48.88 151.12 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U A 4 " pdb=" C1' U A 4 " pdb=" N1 U A 4 " pdb=" C2 U A 4 " ideal model delta sinusoidal sigma weight residual 200.00 57.06 142.94 1 1.50e+01 4.44e-03 7.67e+01 ... (remaining 32711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 8855 0.043 - 0.086: 773 0.086 - 0.129: 180 0.129 - 0.171: 35 0.171 - 0.214: 12 Chirality restraints: 9855 Sorted by residual: chirality pdb=" C3' A A 802 " pdb=" C4' A A 802 " pdb=" O3' A A 802 " pdb=" C2' A A 802 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3' G A 484 " pdb=" C4' G A 484 " pdb=" O3' G A 484 " pdb=" C2' G A 484 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' U A1528 " pdb=" C4' U A1528 " pdb=" O3' U A1528 " pdb=" C2' U A1528 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 9852 not shown) Planarity restraints: 4028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 748 " 0.027 2.00e-02 2.50e+03 1.28e-02 4.93e+00 pdb=" N9 G A 748 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G A 748 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 748 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 748 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 748 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G A 748 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G A 748 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G A 748 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 748 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 748 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 748 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1319 " 0.023 2.00e-02 2.50e+03 1.19e-02 3.87e+00 pdb=" N9 A A1319 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A A1319 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A A1319 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A A1319 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A1319 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A A1319 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A A1319 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1319 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1319 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A A1319 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 745 " 0.021 2.00e-02 2.50e+03 1.11e-02 3.70e+00 pdb=" N9 G A 745 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G A 745 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 745 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 745 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 745 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A 745 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G A 745 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 745 " 0.013 2.00e-02 2.50e+03 pdb=" N2 G A 745 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G A 745 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 745 " 0.001 2.00e-02 2.50e+03 ... (remaining 4025 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 2432 2.67 - 3.23: 39972 3.23 - 3.79: 89640 3.79 - 4.34: 115137 4.34 - 4.90: 154809 Nonbonded interactions: 401990 Sorted by model distance: nonbonded pdb=" OP1 G A 126 " pdb=" O2' U A 605 " model vdw 2.113 2.440 nonbonded pdb=" N6 A A 71 " pdb=" O2 C A 99 " model vdw 2.146 2.520 nonbonded pdb=" OG1 THR E 79 " pdb=" O ASN E 121 " model vdw 2.159 2.440 nonbonded pdb=" OP1 U A 123 " pdb=" O2' C A 311 " model vdw 2.159 2.440 nonbonded pdb=" O2' A A 767 " pdb=" O2' C A1524 " model vdw 2.175 2.440 ... (remaining 401985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.050 Extract box with map and model: 8.550 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 158.640 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 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 : 0.002 0.046 51060 Z= 0.102 Angle : 0.467 10.661 76625 Z= 0.251 Chirality : 0.028 0.214 9855 Planarity : 0.003 0.028 4028 Dihedral : 23.244 179.873 29252 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -4.28 (0.16), residues: 1833 helix: -2.44 (0.18), residues: 532 sheet: -2.16 (0.31), residues: 245 loop : -3.36 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 166 HIS 0.005 0.001 HIS J 15 PHE 0.011 0.001 PHE S 9 TYR 0.017 0.001 TYR D 3 ARG 0.002 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7361 (tm-30) REVERT: D 88 ASN cc_start: 0.5746 (t0) cc_final: 0.5507 (t0) REVERT: E 151 MET cc_start: 0.4923 (mmm) cc_final: 0.4565 (ttm) REVERT: J 80 THR cc_start: 0.3416 (p) cc_final: 0.3073 (p) REVERT: N 60 ARG cc_start: 0.4010 (pmt170) cc_final: 0.3542 (tpp-160) REVERT: P 52 LEU cc_start: 0.6490 (mp) cc_final: 0.6286 (mp) REVERT: S 33 TRP cc_start: 0.4548 (m-90) cc_final: 0.4276 (m100) REVERT: S 75 PRO cc_start: 0.7651 (Cg_endo) cc_final: 0.7406 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.7531 time to fit residues: 523.4334 Evaluate side-chains 300 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 197 HIS E 18 ASN E 77 ASN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN H 117 GLN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN L 28 GLN ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN N 70 HIS ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN T 51 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 51060 Z= 0.363 Angle : 0.909 19.027 76625 Z= 0.454 Chirality : 0.045 0.280 9855 Planarity : 0.007 0.066 4028 Dihedral : 24.156 179.062 26020 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 5.77 % Allowed : 18.49 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.06 (0.17), residues: 1833 helix: -2.05 (0.19), residues: 545 sheet: -2.44 (0.26), residues: 306 loop : -3.24 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 43 HIS 0.019 0.003 HIS S 13 PHE 0.031 0.004 PHE Q 27 TYR 0.028 0.003 TYR C 192 ARG 0.024 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 325 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6359 (pptt) REVERT: C 109 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6555 (mm-30) REVERT: C 139 ASN cc_start: 0.7521 (m110) cc_final: 0.7210 (m-40) REVERT: C 192 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.5446 (p90) REVERT: D 70 GLN cc_start: 0.8177 (tt0) cc_final: 0.7968 (mt0) REVERT: F 5 GLU cc_start: 0.6885 (mp0) cc_final: 0.6608 (mp0) REVERT: F 52 ASN cc_start: 0.5904 (t0) cc_final: 0.5628 (t0) REVERT: H 37 ASN cc_start: 0.6943 (m-40) cc_final: 0.6709 (m-40) REVERT: N 8 ARG cc_start: 0.5389 (mmt180) cc_final: 0.5055 (mmt90) REVERT: N 60 ARG cc_start: 0.5387 (pmt170) cc_final: 0.4103 (tpp-160) REVERT: O 32 THR cc_start: 0.5733 (p) cc_final: 0.5532 (p) REVERT: S 14 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6263 (pp) outliers start: 78 outliers final: 52 residues processed: 373 average time/residue: 0.6798 time to fit residues: 397.4408 Evaluate side-chains 328 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 273 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 266 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 77 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS N 42 ASN N 48 GLN N 61 ASN O 36 ASN O 41 HIS O 61 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS T 51 ASN T 69 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 51060 Z= 0.171 Angle : 0.619 13.738 76625 Z= 0.314 Chirality : 0.035 0.248 9855 Planarity : 0.005 0.087 4028 Dihedral : 23.804 176.953 26020 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.44 % Allowed : 23.59 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.18), residues: 1833 helix: -1.24 (0.21), residues: 548 sheet: -2.05 (0.27), residues: 299 loop : -3.03 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 72 HIS 0.009 0.002 HIS K 23 PHE 0.025 0.002 PHE N 72 TYR 0.022 0.002 TYR L 94 ARG 0.013 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 304 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 ASN cc_start: 0.7776 (p0) cc_final: 0.7575 (p0) REVERT: D 131 ILE cc_start: 0.8237 (mp) cc_final: 0.7868 (mt) REVERT: F 9 MET cc_start: 0.7923 (pmm) cc_final: 0.7672 (pmm) REVERT: F 52 ASN cc_start: 0.6025 (t0) cc_final: 0.5803 (t0) REVERT: H 95 MET cc_start: 0.3625 (tpp) cc_final: 0.1553 (mtp) REVERT: J 81 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7074 (tp30) REVERT: J 85 ASP cc_start: 0.4432 (m-30) cc_final: 0.4121 (t0) REVERT: K 36 ARG cc_start: 0.5946 (mtt180) cc_final: 0.5739 (mtt180) REVERT: L 11 ARG cc_start: 0.6459 (mmt-90) cc_final: 0.6225 (tpt170) REVERT: L 66 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6061 (mt) REVERT: N 60 ARG cc_start: 0.5242 (pmt170) cc_final: 0.4714 (tpm170) REVERT: S 12 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5246 (pp) REVERT: S 65 MET cc_start: 0.1439 (mtt) cc_final: 0.1114 (mmt) outliers start: 60 outliers final: 37 residues processed: 343 average time/residue: 0.6980 time to fit residues: 378.5010 Evaluate side-chains 305 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 266 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 20 LYS Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 60 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 3.9990 chunk 225 optimal weight: 40.0000 chunk 155 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS E 77 ASN J 20 GLN J 56 HIS ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 51060 Z= 0.437 Angle : 1.066 26.003 76625 Z= 0.529 Chirality : 0.053 0.337 9855 Planarity : 0.008 0.141 4028 Dihedral : 24.837 179.332 26020 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.88 % Favored : 83.91 % Rotamer: Outliers : 8.88 % Allowed : 24.85 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.17), residues: 1833 helix: -1.71 (0.20), residues: 534 sheet: -2.37 (0.28), residues: 290 loop : -3.31 (0.17), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP Q 72 HIS 0.026 0.004 HIS K 23 PHE 0.027 0.004 PHE S 40 TYR 0.031 0.003 TYR C 167 ARG 0.055 0.002 ARG P 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 291 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8289 (pp) REVERT: C 48 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6249 (pptt) REVERT: C 155 ARG cc_start: 0.5693 (mmp80) cc_final: 0.5438 (mmp80) REVERT: C 192 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5588 (p90) REVERT: D 135 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 170 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6919 (pp) REVERT: E 10 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (pp) REVERT: E 61 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6276 (mmtt) REVERT: E 81 GLN cc_start: 0.4732 (OUTLIER) cc_final: 0.3762 (pt0) REVERT: F 9 MET cc_start: 0.7273 (pmm) cc_final: 0.6957 (pmm) REVERT: K 36 ARG cc_start: 0.6534 (mtt180) cc_final: 0.5953 (mtt180) REVERT: L 11 ARG cc_start: 0.6542 (mmt-90) cc_final: 0.6266 (tpt170) REVERT: N 60 ARG cc_start: 0.4666 (pmt170) cc_final: 0.4365 (tpm170) REVERT: P 70 ARG cc_start: 0.7695 (tpt-90) cc_final: 0.7122 (tpt170) REVERT: Q 37 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6726 (tp) REVERT: S 12 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5612 (pp) REVERT: S 14 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5833 (pp) REVERT: S 64 GLU cc_start: 0.2735 (OUTLIER) cc_final: 0.2445 (tt0) REVERT: S 65 MET cc_start: 0.0966 (mtt) cc_final: -0.0008 (mmp) outliers start: 120 outliers final: 71 residues processed: 377 average time/residue: 0.6372 time to fit residues: 380.3915 Evaluate side-chains 347 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 265 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 64 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN E 77 ASN E 120 HIS J 56 HIS K 23 HIS K 28 ASN L 95 HIS N 42 ASN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS S 42 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 51060 Z= 0.225 Angle : 0.734 15.043 76625 Z= 0.374 Chirality : 0.041 0.276 9855 Planarity : 0.005 0.084 4028 Dihedral : 24.372 178.736 26020 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 6.73 % Allowed : 28.48 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.18), residues: 1833 helix: -1.28 (0.21), residues: 543 sheet: -2.26 (0.28), residues: 290 loop : -3.19 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 169 HIS 0.015 0.002 HIS O 41 PHE 0.029 0.002 PHE N 72 TYR 0.021 0.002 TYR C 41 ARG 0.017 0.001 ARG K 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 300 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8156 (pp) REVERT: D 94 GLU cc_start: 0.6808 (tp30) cc_final: 0.5791 (tp30) REVERT: D 135 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7145 (tm-30) REVERT: F 9 MET cc_start: 0.7302 (pmm) cc_final: 0.7013 (pmm) REVERT: F 75 GLU cc_start: 0.0223 (OUTLIER) cc_final: -0.0303 (tt0) REVERT: H 110 MET cc_start: 0.5543 (tpt) cc_final: 0.4944 (tpt) REVERT: K 36 ARG cc_start: 0.6330 (mtt180) cc_final: 0.6114 (mtt180) REVERT: L 11 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6630 (tpt170) REVERT: N 60 ARG cc_start: 0.4553 (pmt170) cc_final: 0.3935 (tpm170) REVERT: O 41 HIS cc_start: 0.4668 (OUTLIER) cc_final: 0.4454 (t-170) REVERT: P 28 ARG cc_start: 0.8506 (tmm-80) cc_final: 0.8297 (ttm-80) REVERT: Q 37 ILE cc_start: 0.6950 (tp) cc_final: 0.6700 (tp) REVERT: Q 61 ARG cc_start: 0.7570 (ptt-90) cc_final: 0.7186 (ptt-90) REVERT: S 12 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5456 (pp) REVERT: S 14 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6414 (pp) outliers start: 91 outliers final: 61 residues processed: 360 average time/residue: 0.6423 time to fit residues: 367.3130 Evaluate side-chains 341 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 275 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 167 optimal weight: 0.6980 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 51060 Z= 0.283 Angle : 0.811 17.704 76625 Z= 0.410 Chirality : 0.043 0.271 9855 Planarity : 0.006 0.096 4028 Dihedral : 24.522 179.635 26020 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Rotamer: Outliers : 8.28 % Allowed : 28.92 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.18), residues: 1833 helix: -1.29 (0.20), residues: 550 sheet: -2.21 (0.29), residues: 271 loop : -3.16 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP Q 72 HIS 0.037 0.003 HIS K 23 PHE 0.023 0.002 PHE N 72 TYR 0.024 0.002 TYR L 94 ARG 0.009 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 293 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8153 (pp) REVERT: C 175 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.5731 (t70) REVERT: D 34 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6898 (pt0) REVERT: D 94 GLU cc_start: 0.6836 (tp30) cc_final: 0.6341 (tp30) REVERT: D 135 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 170 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6842 (pp) REVERT: E 61 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6032 (mmtt) REVERT: F 4 TYR cc_start: -0.1687 (OUTLIER) cc_final: -0.2956 (m-80) REVERT: F 9 MET cc_start: 0.7212 (pmm) cc_final: 0.6893 (pmm) REVERT: F 75 GLU cc_start: 0.0488 (OUTLIER) cc_final: 0.0028 (tt0) REVERT: H 9 MET cc_start: 0.4840 (tpp) cc_final: 0.4345 (tpp) REVERT: H 110 MET cc_start: 0.5729 (tpt) cc_final: 0.4805 (tpt) REVERT: K 36 ARG cc_start: 0.6367 (mtt180) cc_final: 0.6154 (mtt180) REVERT: L 11 ARG cc_start: 0.6735 (mmt-90) cc_final: 0.6394 (tpt170) REVERT: O 82 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6253 (mt-10) REVERT: R 62 ARG cc_start: 0.4049 (tpp80) cc_final: 0.2814 (mtt180) REVERT: S 12 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5551 (pp) REVERT: S 14 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6186 (pp) REVERT: S 65 MET cc_start: 0.0451 (mtt) cc_final: -0.0485 (mmp) outliers start: 112 outliers final: 75 residues processed: 370 average time/residue: 0.6421 time to fit residues: 378.5349 Evaluate side-chains 363 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 279 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 39 ASN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 317 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 193 optimal weight: 0.0870 chunk 146 optimal weight: 10.0000 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN K 14 GLN ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 51060 Z= 0.217 Angle : 0.713 14.929 76625 Z= 0.362 Chirality : 0.040 0.277 9855 Planarity : 0.005 0.070 4028 Dihedral : 24.362 178.225 26020 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 7.91 % Allowed : 30.70 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.18), residues: 1833 helix: -1.01 (0.21), residues: 551 sheet: -2.32 (0.28), residues: 298 loop : -3.01 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 17 HIS 0.012 0.002 HIS K 23 PHE 0.038 0.002 PHE N 72 TYR 0.018 0.002 TYR C 192 ARG 0.010 0.001 ARG P 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 295 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8079 (pp) REVERT: C 130 ARG cc_start: 0.6311 (ptm160) cc_final: 0.6092 (ptm160) REVERT: C 192 TYR cc_start: 0.5902 (OUTLIER) cc_final: 0.5485 (p90) REVERT: D 94 GLU cc_start: 0.6657 (tp30) cc_final: 0.5832 (tp30) REVERT: D 135 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 170 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6835 (pp) REVERT: E 53 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7942 (mtt90) REVERT: E 92 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.4041 (mmt180) REVERT: F 4 TYR cc_start: -0.1739 (OUTLIER) cc_final: -0.3410 (m-80) REVERT: F 9 MET cc_start: 0.7227 (pmm) cc_final: 0.6897 (pmm) REVERT: F 75 GLU cc_start: 0.0620 (OUTLIER) cc_final: 0.0143 (tt0) REVERT: H 9 MET cc_start: 0.4549 (tpp) cc_final: 0.3807 (tpp) REVERT: H 95 MET cc_start: 0.3947 (tpp) cc_final: 0.1914 (mtt) REVERT: H 110 MET cc_start: 0.5669 (tpt) cc_final: 0.4693 (tpt) REVERT: J 56 HIS cc_start: 0.6005 (OUTLIER) cc_final: 0.4478 (t-90) REVERT: L 66 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6119 (mt) REVERT: P 42 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6356 (mm) REVERT: R 62 ARG cc_start: 0.3566 (tpp80) cc_final: 0.2653 (ptt180) REVERT: S 12 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5526 (pp) REVERT: S 65 MET cc_start: 0.0025 (mtt) cc_final: -0.0698 (mmp) outliers start: 107 outliers final: 76 residues processed: 365 average time/residue: 0.6599 time to fit residues: 386.7814 Evaluate side-chains 367 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 281 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 39 ASN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN D 73 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN K 23 HIS K 28 ASN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 51060 Z= 0.320 Angle : 0.877 19.079 76625 Z= 0.441 Chirality : 0.046 0.274 9855 Planarity : 0.007 0.098 4028 Dihedral : 24.763 179.800 26020 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.26 % Favored : 83.74 % Rotamer: Outliers : 8.58 % Allowed : 30.18 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.18), residues: 1833 helix: -1.31 (0.20), residues: 548 sheet: -2.46 (0.28), residues: 294 loop : -3.11 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP Q 72 HIS 0.014 0.002 HIS J 15 PHE 0.033 0.003 PHE N 72 TYR 0.022 0.003 TYR C 167 ARG 0.016 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 283 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.6010 (pptt) REVERT: C 192 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5466 (p90) REVERT: D 34 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6826 (pt0) REVERT: D 94 GLU cc_start: 0.6688 (tp30) cc_final: 0.5946 (tp30) REVERT: D 123 MET cc_start: 0.7438 (mmm) cc_final: 0.7199 (tpt) REVERT: D 135 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7297 (tm-30) REVERT: D 170 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6889 (pp) REVERT: E 61 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6470 (mmtt) REVERT: E 92 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.4211 (mmt180) REVERT: F 4 TYR cc_start: -0.1573 (OUTLIER) cc_final: -0.3261 (m-80) REVERT: F 9 MET cc_start: 0.6958 (pmm) cc_final: 0.6609 (pmm) REVERT: H 9 MET cc_start: 0.4678 (tpp) cc_final: 0.4453 (tpp) REVERT: H 110 MET cc_start: 0.5530 (tpt) cc_final: 0.5119 (tpt) REVERT: J 56 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.4535 (t-90) REVERT: J 97 ASP cc_start: 0.3227 (p0) cc_final: 0.2886 (p0) REVERT: N 58 ARG cc_start: 0.6178 (tpp80) cc_final: 0.5535 (tpp80) REVERT: N 60 ARG cc_start: 0.5272 (pmt170) cc_final: 0.4148 (tpp-160) REVERT: P 70 ARG cc_start: 0.7667 (tpt-90) cc_final: 0.7141 (tpt170) REVERT: R 62 ARG cc_start: 0.3544 (tpp80) cc_final: 0.2520 (mtt180) REVERT: S 12 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5293 (pp) REVERT: S 65 MET cc_start: 0.1033 (mtt) cc_final: 0.0825 (mtt) REVERT: T 51 ASN cc_start: 0.7501 (m-40) cc_final: 0.7271 (m110) outliers start: 116 outliers final: 82 residues processed: 354 average time/residue: 0.6340 time to fit residues: 360.9577 Evaluate side-chains 359 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 268 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 82 LYS Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 0.2980 chunk 303 optimal weight: 2.9990 chunk 277 optimal weight: 30.0000 chunk 295 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN P 26 ASN ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 51060 Z= 0.160 Angle : 0.661 13.789 76625 Z= 0.336 Chirality : 0.037 0.256 9855 Planarity : 0.005 0.079 4028 Dihedral : 24.290 177.710 26020 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 5.10 % Allowed : 33.80 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.19), residues: 1833 helix: -0.63 (0.22), residues: 552 sheet: -2.06 (0.29), residues: 281 loop : -2.89 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 17 HIS 0.030 0.002 HIS K 23 PHE 0.040 0.002 PHE N 72 TYR 0.016 0.001 TYR D 50 ARG 0.009 0.001 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 304 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6792 (pp) REVERT: E 70 MET cc_start: 0.5493 (tpp) cc_final: 0.5283 (tpp) REVERT: E 92 ARG cc_start: 0.6046 (OUTLIER) cc_final: 0.4046 (mmt180) REVERT: F 4 TYR cc_start: -0.1641 (OUTLIER) cc_final: -0.3353 (m-80) REVERT: F 9 MET cc_start: 0.7205 (pmm) cc_final: 0.6860 (pmm) REVERT: H 9 MET cc_start: 0.4486 (tpp) cc_final: 0.4157 (tpp) REVERT: H 37 ASN cc_start: 0.6834 (m-40) cc_final: 0.6618 (m-40) REVERT: H 48 PHE cc_start: 0.4370 (p90) cc_final: 0.4006 (p90) REVERT: H 110 MET cc_start: 0.5431 (tpt) cc_final: 0.4532 (tpt) REVERT: J 97 ASP cc_start: 0.2717 (p0) cc_final: 0.2389 (p0) REVERT: K 84 MET cc_start: 0.5144 (ttt) cc_final: 0.4660 (tmm) REVERT: N 22 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6903 (ptpp) REVERT: N 80 ARG cc_start: 0.7630 (tmm-80) cc_final: 0.7410 (tmm-80) REVERT: P 34 GLU cc_start: 0.7552 (pm20) cc_final: 0.7333 (pm20) REVERT: P 42 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6205 (mm) REVERT: Q 29 LYS cc_start: 0.6301 (mmmt) cc_final: 0.5897 (ptmt) REVERT: Q 32 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7336 (tp) REVERT: R 62 ARG cc_start: 0.3769 (tpp80) cc_final: 0.2746 (mtt180) REVERT: S 12 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5550 (pp) REVERT: S 54 ARG cc_start: 0.5582 (tpp80) cc_final: 0.5326 (tpp80) REVERT: T 59 ARG cc_start: 0.7307 (tpp80) cc_final: 0.6828 (mmm-85) outliers start: 69 outliers final: 48 residues processed: 343 average time/residue: 0.6726 time to fit residues: 368.4081 Evaluate side-chains 337 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 282 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 1.9990 chunk 312 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 327 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 160 optimal weight: 0.0870 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN K 23 HIS L 4 ASN ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 51060 Z= 0.156 Angle : 0.641 13.482 76625 Z= 0.324 Chirality : 0.035 0.237 9855 Planarity : 0.005 0.101 4028 Dihedral : 24.178 179.298 26020 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 4.88 % Allowed : 34.69 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.89 (0.19), residues: 1833 helix: -0.40 (0.22), residues: 551 sheet: -2.15 (0.29), residues: 290 loop : -2.84 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 17 HIS 0.013 0.001 HIS J 15 PHE 0.041 0.002 PHE C 202 TYR 0.013 0.001 TYR D 50 ARG 0.033 0.001 ARG P 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 287 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6765 (tm-30) REVERT: D 170 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6847 (pp) REVERT: E 92 ARG cc_start: 0.5948 (OUTLIER) cc_final: 0.3958 (mmt180) REVERT: F 4 TYR cc_start: -0.1761 (OUTLIER) cc_final: -0.3432 (m-80) REVERT: F 9 MET cc_start: 0.7225 (pmm) cc_final: 0.6879 (pmm) REVERT: H 9 MET cc_start: 0.4670 (tpp) cc_final: 0.4212 (tpp) REVERT: H 48 PHE cc_start: 0.4272 (p90) cc_final: 0.3939 (p90) REVERT: H 95 MET cc_start: 0.3810 (tpp) cc_final: 0.2116 (mtt) REVERT: H 110 MET cc_start: 0.5229 (tpt) cc_final: 0.4268 (tpt) REVERT: J 87 LEU cc_start: 0.7251 (mm) cc_final: 0.7004 (mm) REVERT: J 97 ASP cc_start: 0.2994 (p0) cc_final: 0.2634 (p0) REVERT: K 84 MET cc_start: 0.5106 (ttt) cc_final: 0.4005 (tmm) REVERT: N 88 MET cc_start: 0.6899 (mmp) cc_final: 0.6216 (mmp) REVERT: P 42 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6436 (mm) REVERT: Q 29 LYS cc_start: 0.6206 (mmmt) cc_final: 0.5992 (ptmt) REVERT: R 62 ARG cc_start: 0.3362 (tpp80) cc_final: 0.2413 (mtt180) REVERT: S 12 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5419 (pp) REVERT: T 59 ARG cc_start: 0.7228 (tpp80) cc_final: 0.6880 (mmm-85) outliers start: 66 outliers final: 51 residues processed: 325 average time/residue: 0.6478 time to fit residues: 335.2152 Evaluate side-chains 330 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 268 optimal weight: 0.2980 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN K 23 HIS L 4 ASN P 29 ASN ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.162834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.154290 restraints weight = 163596.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.156411 restraints weight = 68578.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.157666 restraints weight = 35476.233| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 51060 Z= 0.292 Angle : 0.760 59.199 76625 Z= 0.403 Chirality : 0.044 2.269 9855 Planarity : 0.006 0.213 4028 Dihedral : 24.175 179.821 26020 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 4.81 % Allowed : 34.54 % Favored : 60.65 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.19), residues: 1833 helix: -0.41 (0.22), residues: 551 sheet: -2.14 (0.29), residues: 290 loop : -2.85 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 17 HIS 0.350 0.006 HIS K 23 PHE 0.037 0.002 PHE N 72 TYR 0.011 0.002 TYR O 68 ARG 0.014 0.001 ARG N 64 =============================================================================== Job complete usr+sys time: 7758.41 seconds wall clock time: 142 minutes 56.65 seconds (8576.65 seconds total)