Starting phenix.real_space_refine (version: dev) on Thu Dec 22 02:37:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/12_2022/6w6k_21558.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/12_2022/6w6k_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_21558/12_2022/6w6k_21558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/12_2022/6w6k_21558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/12_2022/6w6k_21558.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6k_21558/12_2022/6w6k_21558.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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-4807/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: 26.87, per 1000 atoms: 0.57 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: 24.06 Conformation dependent library (CDL) restraints added in 2.9 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: 17.42 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: 42.81 Time building geometry restraints manager: 25.45 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: 26174 35.97 - 71.95: 888 71.95 - 107.92: 76 107.92 - 143.90: 8 143.90 - 179.87: 10 Dihedral angle restraints: 27156 sinusoidal: 21804 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 27153 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 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. 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: 1.010 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: 0.030 Extract box with map and model: 10.240 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.470 Process input model: 155.210 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 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 : 14.659 179.873 23694 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 2.564 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 outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.7750 time to fit residues: 548.9357 Evaluate side-chains 298 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7186 ------------------------------------------------------------------------------- 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: 10.0000 chunk 168 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 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 ** 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 N 42 ASN ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN N 70 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 T 20 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 51060 Z= 0.363 Angle : 0.890 17.941 76625 Z= 0.444 Chirality : 0.045 0.281 9855 Planarity : 0.007 0.059 4028 Dihedral : 16.044 179.546 20462 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer Outliers : 5.25 % 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: -4.05 (0.17), residues: 1833 helix: -2.01 (0.19), residues: 545 sheet: -2.39 (0.26), residues: 309 loop : -3.27 (0.17), residues: 979 *********************** 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 398 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 327 time to evaluate : 2.694 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 outliers start: 71 outliers final: 49 residues processed: 369 average time/residue: 0.6677 time to fit residues: 388.3401 Evaluate side-chains 325 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4301 time to fit residues: 42.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 248 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 266 optimal weight: 0.0570 chunk 296 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 95 HIS N 48 GLN O 36 ASN O 41 HIS O 61 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 51060 Z= 0.148 Angle : 0.583 11.323 76625 Z= 0.297 Chirality : 0.033 0.234 9855 Planarity : 0.005 0.085 4028 Dihedral : 15.249 176.631 20462 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 2.51 % 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: -3.24 (0.18), residues: 1833 helix: -1.08 (0.21), residues: 550 sheet: -1.95 (0.28), residues: 298 loop : -2.95 (0.18), residues: 985 *********************** 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 354 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 2.859 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 outliers start: 34 outliers final: 13 residues processed: 342 average time/residue: 0.6680 time to fit residues: 359.5258 Evaluate side-chains 283 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 270 time to evaluate : 2.663 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4530 time to fit residues: 13.3778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 33 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 300 optimal weight: 0.1980 chunk 318 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 284 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 77 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS L 4 ASN L 72 ASN N 61 ASN O 41 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 51060 Z= 0.157 Angle : 0.588 10.796 76625 Z= 0.298 Chirality : 0.033 0.252 9855 Planarity : 0.005 0.087 4028 Dihedral : 15.253 178.696 20462 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 3.40 % 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: -2.92 (0.19), residues: 1833 helix: -0.63 (0.22), residues: 546 sheet: -1.90 (0.28), residues: 314 loop : -2.82 (0.18), residues: 973 *********************** 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 345 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 299 time to evaluate : 2.791 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 outliers start: 46 outliers final: 24 residues processed: 327 average time/residue: 0.6591 time to fit residues: 343.4481 Evaluate side-chains 301 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 277 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4068 time to fit residues: 21.4355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 219 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** E 77 ASN J 20 GLN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 72 ASN N 61 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: 0.6582 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.124 51060 Z= 0.306 Angle : 0.823 16.831 76625 Z= 0.414 Chirality : 0.043 0.283 9855 Planarity : 0.007 0.110 4028 Dihedral : 16.463 178.809 20462 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.31 % Favored : 86.63 % Rotamer Outliers : 4.44 % 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: -3.31 (0.18), residues: 1833 helix: -1.10 (0.21), residues: 548 sheet: -1.99 (0.29), residues: 289 loop : -3.01 (0.17), residues: 996 *********************** 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 356 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 296 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 336 average time/residue: 0.6817 time to fit residues: 366.2234 Evaluate side-chains 297 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 270 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4349 time to fit residues: 25.4252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 119 HIS E 77 ASN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN L 72 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 51060 Z= 0.368 Angle : 0.936 16.872 76625 Z= 0.471 Chirality : 0.048 0.283 9855 Planarity : 0.007 0.124 4028 Dihedral : 17.511 179.419 20462 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 27.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.17 % Favored : 84.67 % Rotamer Outliers : 5.33 % 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: -3.81 (0.17), residues: 1833 helix: -1.53 (0.20), residues: 554 sheet: -2.50 (0.28), residues: 275 loop : -3.23 (0.17), residues: 1004 *********************** 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 367 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 295 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 41 residues processed: 338 average time/residue: 0.6469 time to fit residues: 345.6310 Evaluate side-chains 314 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 273 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4471 time to fit residues: 35.8132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 232 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 317 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN N 61 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 51060 Z= 0.169 Angle : 0.659 11.116 76625 Z= 0.336 Chirality : 0.037 0.246 9855 Planarity : 0.005 0.096 4028 Dihedral : 16.463 177.811 20462 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.98 % Favored : 89.96 % Rotamer Outliers : 2.00 % 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: -3.18 (0.18), residues: 1833 helix: -0.71 (0.22), residues: 532 sheet: -2.15 (0.28), residues: 309 loop : -3.00 (0.18), residues: 992 *********************** 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 332 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 305 time to evaluate : 2.983 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 outliers start: 27 outliers final: 13 residues processed: 318 average time/residue: 0.6751 time to fit residues: 335.9816 Evaluate side-chains 285 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 272 time to evaluate : 2.596 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4232 time to fit residues: 13.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 51060 Z= 0.254 Angle : 0.743 13.579 76625 Z= 0.375 Chirality : 0.040 0.253 9855 Planarity : 0.006 0.106 4028 Dihedral : 16.744 179.968 20462 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.80 % Favored : 86.14 % Rotamer Outliers : 2.81 % 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: -3.27 (0.18), residues: 1833 helix: -0.90 (0.21), residues: 550 sheet: -2.25 (0.28), residues: 291 loop : -2.99 (0.18), residues: 992 *********************** 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 336 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 321 average time/residue: 0.6763 time to fit residues: 339.1450 Evaluate side-chains 308 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 2.720 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4362 time to fit residues: 22.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 3.9990 chunk 303 optimal weight: 0.6980 chunk 277 optimal weight: 30.0000 chunk 295 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 267 optimal weight: 0.0000 chunk 279 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN L 4 ASN L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN S 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 51060 Z= 0.157 Angle : 0.635 13.404 76625 Z= 0.321 Chirality : 0.035 0.236 9855 Planarity : 0.005 0.091 4028 Dihedral : 16.226 178.653 20462 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.04 % Favored : 89.91 % Rotamer Outliers : 1.33 % 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: -2.98 (0.19), residues: 1833 helix: -0.49 (0.22), residues: 540 sheet: -2.27 (0.28), residues: 309 loop : -2.83 (0.19), residues: 984 *********************** 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 326 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 308 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 318 average time/residue: 0.6785 time to fit residues: 339.6257 Evaluate side-chains 296 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 285 time to evaluate : 2.630 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4055 time to fit residues: 11.2346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 201 optimal weight: 0.0470 chunk 160 optimal weight: 0.3980 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 51060 Z= 0.188 Angle : 0.663 10.965 76625 Z= 0.336 Chirality : 0.036 0.243 9855 Planarity : 0.005 0.093 4028 Dihedral : 16.290 179.855 20462 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.67 % Favored : 88.27 % Rotamer Outliers : 0.96 % 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: -3.03 (0.19), residues: 1833 helix: -0.52 (0.22), residues: 539 sheet: -2.24 (0.29), residues: 291 loop : -2.90 (0.18), residues: 1003 ********************** 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 313 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 300 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 304 average time/residue: 0.6771 time to fit residues: 325.3132 Evaluate side-chains 295 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 288 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4111 time to fit residues: 8.2288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.0470 chunk 278 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 268 optimal weight: 0.0570 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 overall best weight: 3.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN T 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.159584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.151226 restraints weight = 166290.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.153267 restraints weight = 70467.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.154446 restraints weight = 36653.931| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 51060 Z= 0.265 Angle : 0.778 13.705 76625 Z= 0.392 Chirality : 0.041 0.253 9855 Planarity : 0.006 0.102 4028 Dihedral : 16.864 179.396 20462 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.18 % Favored : 85.76 % Rotamer Outliers : 1.18 % 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: -3.32 (0.18), residues: 1833 helix: -0.89 (0.21), residues: 545 sheet: -2.25 (0.29), residues: 284 loop : -3.07 (0.17), residues: 1004 =============================================================================== Job complete usr+sys time: 7274.52 seconds wall clock time: 134 minutes 37.85 seconds (8077.85 seconds total)