Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 18:25:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/07_2023/6uh5_20767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/07_2023/6uh5_20767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/07_2023/6uh5_20767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/07_2023/6uh5_20767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/07_2023/6uh5_20767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/07_2023/6uh5_20767_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.002 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 Zn 1 6.06 5 P 292 5.49 5 S 79 5.16 5 C 14533 2.51 5 N 4361 2.21 5 O 5200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K ASP 159": "OD1" <-> "OD2" Residue "K ASP 174": "OD1" <-> "OD2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 275": "OD1" <-> "OD2" Residue "K PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 736": "NH1" <-> "NH2" Residue "M ASP 737": "OD1" <-> "OD2" Residue "M PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 768": "OD1" <-> "OD2" Residue "M PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 864": "NH1" <-> "NH2" Residue "M TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 882": "OE1" <-> "OE2" Residue "M TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 890": "OE1" <-> "OE2" Residue "M PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 919": "OE1" <-> "OE2" Residue "M PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 963": "OD1" <-> "OD2" Residue "M TYR 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 977": "OE1" <-> "OE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "N TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 74": "NH1" <-> "NH2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 115": "OD1" <-> "OD2" Residue "N TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 146": "OD1" <-> "OD2" Residue "N ARG 147": "NH1" <-> "NH2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "N ASP 270": "OD1" <-> "OD2" Residue "N TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 306": "OE1" <-> "OE2" Residue "N ASP 320": "OD1" <-> "OD2" Residue "N ASP 362": "OD1" <-> "OD2" Residue "N GLU 367": "OE1" <-> "OE2" Residue "N ASP 371": "OD1" <-> "OD2" Residue "N GLU 374": "OE1" <-> "OE2" Residue "N GLU 378": "OE1" <-> "OE2" Residue "N PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 410": "NH1" <-> "NH2" Residue "N ASP 413": "OD1" <-> "OD2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q ASP 21": "OD1" <-> "OD2" Residue "Q ASP 32": "OD1" <-> "OD2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X GLU 300": "OE1" <-> "OE2" Residue "L TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L ASP 93": "OD1" <-> "OD2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L ASP 111": "OD1" <-> "OD2" Residue "L ARG 140": "NH1" <-> "NH2" Residue "L ASP 152": "OD1" <-> "OD2" Residue "L ASP 184": "OD1" <-> "OD2" Residue "L PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L ARG 209": "NH1" <-> "NH2" Residue "L GLU 230": "OE1" <-> "OE2" Residue "L PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 240": "OE1" <-> "OE2" Residue "L ASP 247": "OD1" <-> "OD2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 263": "OD1" <-> "OD2" Residue "L ASP 277": "OD1" <-> "OD2" Residue "L ASP 278": "OD1" <-> "OD2" Residue "L TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 284": "OE1" <-> "OE2" Residue "L GLU 291": "OE1" <-> "OE2" Residue "L PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 320": "OE1" <-> "OE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 347": "NH1" <-> "NH2" Residue "L TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 370": "OE1" <-> "OE2" Residue "L PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 377": "OD1" <-> "OD2" Residue "L ASP 379": "OD1" <-> "OD2" Residue "L ASP 385": "OD1" <-> "OD2" Residue "L ASP 394": "OD1" <-> "OD2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "O ARG 116": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 24466 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 722 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2365 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1775 Classifications: {'peptide': 222} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 212} Chain breaks: 2 Chain: "N" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3273 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 63 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "X" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 604 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Chain: "L" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3128 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "P" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 329 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16028 SG CYS M 988 100.644 72.149 42.184 1.00142.90 S ATOM 16042 SG CYS M 990 95.749 71.558 42.382 1.00156.46 S ATOM 16070 SG CYS M 995 98.805 74.904 40.292 1.00160.65 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N MET R 4 " occ=0.84 ... (6 atoms not shown) pdb=" CE MET R 4 " occ=0.84 residue: pdb="ZN ZN M1101 " occ=0.41 Time building chain proxies: 11.43, per 1000 atoms: 0.47 Number of scatterers: 24466 At special positions: 0 Unit cell: (174.24, 134.112, 130.944, 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) Zn 1 29.99 S 79 16.00 P 292 15.00 O 5200 8.00 N 4361 7.00 C 14533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS Q 76 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.72 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M1101 " pdb="ZN ZN M1101 " - pdb=" SG CYS M 995 " pdb="ZN ZN M1101 " - pdb=" SG CYS M 988 " pdb="ZN ZN M1101 " - pdb=" SG CYS M 990 " 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 27 sheets defined 29.2% alpha, 13.0% beta 131 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 10.44 Creating SS restraints... Processing helix chain 'A' and resid 47 through 54 removed outlier: 4.075A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.078A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.812A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.566A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 removed outlier: 3.923A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.122A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.684A pdb=" N LEU C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.591A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.693A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.840A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 77 removed outlier: 3.901A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.747A pdb=" N GLN D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.568A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.640A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.831A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 113 removed outlier: 3.979A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 4.179A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.619A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 28 through 33 Processing helix chain 'G' and resid 47 through 71 Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.749A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.875A pdb=" N SER H 57 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE H 58 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN H 60 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL H 63 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN H 64 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE H 67 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA H 71 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY H 72 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA H 74 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 76 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA H 78 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS H 79 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 98 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.800A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 738 removed outlier: 4.043A pdb=" N ILE M 735 " --> pdb=" O GLN M 731 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN M 738 " --> pdb=" O ILE M 734 " (cutoff:3.500A) Processing helix chain 'M' and resid 820 through 831 removed outlier: 3.509A pdb=" N PHE M 830 " --> pdb=" O PHE M 826 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN M 831 " --> pdb=" O GLN M 827 " (cutoff:3.500A) Processing helix chain 'M' and resid 894 through 906 removed outlier: 3.864A pdb=" N ILE M 905 " --> pdb=" O GLU M 901 " (cutoff:3.500A) Processing helix chain 'M' and resid 931 through 934 Processing helix chain 'N' and resid 4 through 7 No H-bonds generated for 'chain 'N' and resid 4 through 7' Processing helix chain 'N' and resid 356 through 358 No H-bonds generated for 'chain 'N' and resid 356 through 358' Processing helix chain 'N' and resid 428 through 431 No H-bonds generated for 'chain 'N' and resid 428 through 431' Processing helix chain 'Q' and resid 23 through 34 Processing helix chain 'Q' and resid 38 through 40 No H-bonds generated for 'chain 'Q' and resid 38 through 40' Processing helix chain 'Q' and resid 57 through 59 No H-bonds generated for 'chain 'Q' and resid 57 through 59' Processing helix chain 'X' and resid 201 through 210 removed outlier: 4.058A pdb=" N VAL X 205 " --> pdb=" O GLU X 201 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL X 210 " --> pdb=" O ILE X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 212 through 225 removed outlier: 4.567A pdb=" N LEU X 220 " --> pdb=" O VAL X 216 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER X 221 " --> pdb=" O ASN X 217 " (cutoff:3.500A) Proline residue: X 222 - end of helix removed outlier: 4.202A pdb=" N ASN X 225 " --> pdb=" O SER X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 295 through 307 removed outlier: 3.655A pdb=" N GLU X 300 " --> pdb=" O ASN X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 309 through 312 No H-bonds generated for 'chain 'X' and resid 309 through 312' Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.220A pdb=" N THR X 320 " --> pdb=" O ILE X 316 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN X 321 " --> pdb=" O SER X 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 210 removed outlier: 3.555A pdb=" N GLN L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 236 Processing helix chain 'L' and resid 368 through 370 No H-bonds generated for 'chain 'L' and resid 368 through 370' Processing helix chain 'L' and resid 383 through 402 removed outlier: 3.534A pdb=" N TYR L 387 " --> pdb=" O LEU L 383 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE L 395 " --> pdb=" O ILE L 391 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 94 removed outlier: 3.514A pdb=" N TYR O 90 " --> pdb=" O THR O 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU O 91 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 106 removed outlier: 3.684A pdb=" N ILE O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 125 removed outlier: 3.507A pdb=" N LEU O 122 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA O 125 " --> pdb=" O PHE O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 87 through 94 removed outlier: 4.120A pdb=" N LEU P 91 " --> pdb=" O ARG P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 Processing helix chain 'P' and resid 115 through 121 Processing sheet with id= A, first strand: chain 'K' and resid 60 through 65 removed outlier: 3.750A pdb=" N ASP K 50 " --> pdb=" O GLN K 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 83 through 87 removed outlier: 5.793A pdb=" N HIS K 97 " --> pdb=" O ARG K 102 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG K 102 " --> pdb=" O HIS K 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.660A pdb=" N LEU K 125 " --> pdb=" O TRP K 137 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP K 137 " --> pdb=" O LEU K 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 157 through 159 removed outlier: 3.578A pdb=" N SER K 157 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP K 181 " --> pdb=" O CYS K 187 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS K 187 " --> pdb=" O ASP K 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 206 through 211 removed outlier: 6.756A pdb=" N LYS K 221 " --> pdb=" O SER K 207 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL K 209 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU K 219 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG K 239 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU K 231 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL K 237 " --> pdb=" O GLU K 231 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 258 through 260 Processing sheet with id= G, first strand: chain 'K' and resid 18 through 22 removed outlier: 6.944A pdb=" N LEU K 323 " --> pdb=" O ASP K 20 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 279 through 282 removed outlier: 3.804A pdb=" N GLN K 291 " --> pdb=" O VAL K 281 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 861 through 864 Processing sheet with id= J, first strand: chain 'M' and resid 885 through 887 removed outlier: 3.966A pdb=" N ILE M 885 " --> pdb=" O ILE M 958 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE M 956 " --> pdb=" O TYR M 887 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG M 953 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 890 through 893 removed outlier: 3.888A pdb=" N ASP M 918 " --> pdb=" O THR M 921 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE M 923 " --> pdb=" O ARG M 916 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG M 916 " --> pdb=" O ILE M 923 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 32 through 35 removed outlier: 4.354A pdb=" N ILE N 51 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU N 65 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA N 63 " --> pdb=" O ILE N 53 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP N 55 " --> pdb=" O PRO N 61 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 97 through 101 Processing sheet with id= N, first strand: chain 'N' and resid 121 through 123 removed outlier: 3.778A pdb=" N VAL N 131 " --> pdb=" O TYR N 140 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR N 140 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE N 154 " --> pdb=" O VAL N 141 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR N 143 " --> pdb=" O HIS N 152 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS N 152 " --> pdb=" O THR N 143 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 171 through 174 removed outlier: 3.746A pdb=" N VAL N 171 " --> pdb=" O GLY N 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 183 " --> pdb=" O CYS N 173 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU N 212 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR N 210 " --> pdb=" O ALA N 193 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN N 195 " --> pdb=" O CYS N 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS N 208 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 221 through 224 removed outlier: 3.780A pdb=" N GLN N 221 " --> pdb=" O ASN N 234 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE N 231 " --> pdb=" O TYR N 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS N 266 " --> pdb=" O GLN N 242 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN N 244 " --> pdb=" O LEU N 264 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU N 264 " --> pdb=" O GLN N 244 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'N' and resid 280 through 282 Processing sheet with id= R, first strand: chain 'N' and resid 326 through 329 removed outlier: 6.184A pdb=" N SER N 349 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU N 20 " --> pdb=" O SER N 349 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 43 through 45 removed outlier: 4.830A pdb=" N LEU Q 43 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 52 through 55 removed outlier: 3.811A pdb=" N ILE L 249 " --> pdb=" O GLU L 260 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 57 through 59 Processing sheet with id= V, first strand: chain 'L' and resid 88 through 90 Processing sheet with id= W, first strand: chain 'L' and resid 122 through 124 Processing sheet with id= X, first strand: chain 'L' and resid 155 through 157 removed outlier: 3.720A pdb=" N SER L 139 " --> pdb=" O TYR L 351 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 352 " --> pdb=" O VAL L 112 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL L 112 " --> pdb=" O ALA L 352 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU L 354 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER L 110 " --> pdb=" O LEU L 354 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 165 through 167 Processing sheet with id= Z, first strand: chain 'L' and resid 271 through 274 removed outlier: 4.066A pdb=" N ASP L 274 " --> pdb=" O MET L 279 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET L 279 " --> pdb=" O ASP L 274 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 28 through 34 removed outlier: 7.011A pdb=" N TYR L 39 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG L 33 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 12.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4078 1.32 - 1.45: 8645 1.45 - 1.58: 12124 1.58 - 1.71: 559 1.71 - 1.84: 119 Bond restraints: 25525 Sorted by residual: bond pdb=" CA THR E 118 " pdb=" CB THR E 118 " ideal model delta sigma weight residual 1.530 1.456 0.073 1.57e-02 4.06e+03 2.19e+01 bond pdb=" N PRO N 9 " pdb=" CD PRO N 9 " ideal model delta sigma weight residual 1.474 1.531 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C SER X 221 " pdb=" N PRO X 222 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" CA PRO Q 37 " pdb=" C PRO Q 37 " ideal model delta sigma weight residual 1.517 1.496 0.021 6.70e-03 2.23e+04 9.86e+00 bond pdb=" C GLN M 894 " pdb=" N PRO M 895 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.30e-02 5.92e+03 8.42e+00 ... (remaining 25520 not shown) Histogram of bond angle deviations from ideal: 71.57 - 87.44: 3 87.44 - 103.32: 821 103.32 - 119.19: 21845 119.19 - 135.06: 13088 135.06 - 150.94: 5 Bond angle restraints: 35762 Sorted by residual: angle pdb=" N LYS M 857 " pdb=" CA LYS M 857 " pdb=" C LYS M 857 " ideal model delta sigma weight residual 111.07 141.71 -30.64 1.07e+00 8.73e-01 8.20e+02 angle pdb=" N ARG L 237 " pdb=" CA ARG L 237 " pdb=" C ARG L 237 " ideal model delta sigma weight residual 110.59 73.97 36.62 1.45e+00 4.76e-01 6.38e+02 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 112.93 140.59 -27.66 1.12e+00 7.97e-01 6.10e+02 angle pdb=" N ARG F 95 " pdb=" CA ARG F 95 " pdb=" C ARG F 95 " ideal model delta sigma weight residual 108.69 71.57 37.12 1.77e+00 3.19e-01 4.40e+02 angle pdb=" N GLY M 952 " pdb=" CA GLY M 952 " pdb=" C GLY M 952 " ideal model delta sigma weight residual 115.30 143.94 -28.64 1.44e+00 4.82e-01 3.96e+02 ... (remaining 35757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 12690 35.43 - 70.87: 1600 70.87 - 106.30: 40 106.30 - 141.74: 1 141.74 - 177.17: 2 Dihedral angle restraints: 14333 sinusoidal: 7576 harmonic: 6757 Sorted by residual: dihedral pdb=" C LEU Q 8 " pdb=" N LEU Q 8 " pdb=" CA LEU Q 8 " pdb=" CB LEU Q 8 " ideal model delta harmonic sigma weight residual -122.60 -158.44 35.84 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N LEU Q 8 " pdb=" C LEU Q 8 " pdb=" CA LEU Q 8 " pdb=" CB LEU Q 8 " ideal model delta harmonic sigma weight residual 122.80 155.81 -33.01 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" N SER L 238 " pdb=" C SER L 238 " pdb=" CA SER L 238 " pdb=" CB SER L 238 " ideal model delta harmonic sigma weight residual 122.80 154.95 -32.15 0 2.50e+00 1.60e-01 1.65e+02 ... (remaining 14330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 4003 0.309 - 0.617: 26 0.617 - 0.926: 7 0.926 - 1.234: 1 1.234 - 1.543: 3 Chirality restraints: 4040 Sorted by residual: chirality pdb=" CA LEU Q 8 " pdb=" N LEU Q 8 " pdb=" C LEU Q 8 " pdb=" CB LEU Q 8 " both_signs ideal model delta sigma weight residual False 2.51 0.97 1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" CA MET N 56 " pdb=" N MET N 56 " pdb=" C MET N 56 " pdb=" CB MET N 56 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.28e+01 chirality pdb=" CA SER L 238 " pdb=" N SER L 238 " pdb=" C SER L 238 " pdb=" CB SER L 238 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.91e+01 ... (remaining 4037 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 310 " 0.059 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO L 311 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO L 311 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 311 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS M 857 " -0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS M 857 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS M 857 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS M 858 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 884 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE M 884 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE M 884 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE M 885 " 0.019 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 79 2.38 - 3.01: 12417 3.01 - 3.64: 39755 3.64 - 4.27: 61287 4.27 - 4.90: 93828 Nonbonded interactions: 207366 Sorted by model distance: nonbonded pdb=" O LEU F 90 " pdb=" O ARG F 95 " model vdw 1.749 3.040 nonbonded pdb=" N ARG L 237 " pdb=" O ARG L 237 " model vdw 1.782 2.496 nonbonded pdb=" N ARG F 95 " pdb=" O ARG F 95 " model vdw 2.000 2.496 nonbonded pdb=" OE1 GLU N 368 " pdb=" NZ LYS Q 11 " model vdw 2.073 2.520 nonbonded pdb=" O ILE K 198 " pdb=" O SER M 907 " model vdw 2.120 3.040 ... (remaining 207361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) } ncs_group { reference = (chain 'D' and (resid 29 through 116 or resid 118 through 121)) selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 116 or resid 118 through 121)) } ncs_group { reference = (chain 'O' and (resid 85 through 106 or resid 113 through 115 or (resid 116 and \ (name N or name CA or name C or name O or name CB )) or resid 117 through 126)) selection = (chain 'P' and resid 85 through 126) } 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=0.41 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 9.220 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 76.790 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.011 0.108 25525 Z= 0.688 Angle : 1.396 37.118 35762 Z= 0.845 Chirality : 0.090 1.543 4040 Planarity : 0.007 0.087 3532 Dihedral : 23.701 177.172 9960 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.48 % Rotamer Outliers : 2.23 % Cbeta Deviations : 1.74 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 1.25 % Twisted General : 0.27 % 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: -4.70 (0.14), residues: 2266 helix: -3.74 (0.12), residues: 732 sheet: -2.73 (0.23), residues: 364 loop : -2.80 (0.15), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 266 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 10 residues processed: 306 average time/residue: 0.4529 time to fit residues: 202.7791 Evaluate side-chains 161 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2104 time to fit residues: 7.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 73 ASN C 112 GLN D 81 ASN E 68 GLN E 113 HIS F 25 ASN G 24 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 HIS K 73 ASN M 743 ASN M 827 GLN M 852 GLN N 149 ASN ** N 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 412 ASN Q 68 HIS X 200 ASN X 322 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 133 HIS L 172 HIS ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 255 ASN L 317 GLN L 325 HIS L 344 ASN L 346 ASN P 92 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 25525 Z= 0.234 Angle : 0.676 8.353 35762 Z= 0.380 Chirality : 0.042 0.180 4040 Planarity : 0.005 0.074 3532 Dihedral : 27.219 177.754 5460 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.15), residues: 2266 helix: -2.06 (0.16), residues: 747 sheet: -2.19 (0.23), residues: 381 loop : -2.39 (0.17), residues: 1138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 229 average time/residue: 0.4084 time to fit residues: 146.1482 Evaluate side-chains 167 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2401 time to fit residues: 11.6064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 30.0000 chunk 71 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 247 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 HIS M 743 ASN ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 ASN L 325 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 25525 Z= 0.302 Angle : 0.655 8.757 35762 Z= 0.365 Chirality : 0.042 0.185 4040 Planarity : 0.005 0.062 3532 Dihedral : 26.969 173.186 5460 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.75 (0.16), residues: 2266 helix: -1.31 (0.17), residues: 755 sheet: -1.88 (0.25), residues: 354 loop : -2.15 (0.17), residues: 1157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 213 average time/residue: 0.3976 time to fit residues: 139.5808 Evaluate side-chains 174 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2149 time to fit residues: 13.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 118 optimal weight: 0.0370 chunk 25 optimal weight: 0.0170 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 112 GLN H 46 HIS ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 300 HIS ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN L 325 HIS P 94 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 25525 Z= 0.177 Angle : 0.591 9.692 35762 Z= 0.330 Chirality : 0.040 0.229 4040 Planarity : 0.004 0.062 3532 Dihedral : 26.697 174.785 5460 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.15 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.16 (0.17), residues: 2266 helix: -0.59 (0.19), residues: 737 sheet: -1.54 (0.26), residues: 343 loop : -1.96 (0.17), residues: 1186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 200 average time/residue: 0.3695 time to fit residues: 117.0336 Evaluate side-chains 170 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2221 time to fit residues: 9.8858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.0010 chunk 138 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 0.0060 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 743 ASN ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 25525 Z= 0.177 Angle : 0.578 8.902 35762 Z= 0.323 Chirality : 0.039 0.178 4040 Planarity : 0.004 0.055 3532 Dihedral : 26.445 173.698 5460 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2266 helix: -0.13 (0.19), residues: 738 sheet: -1.28 (0.27), residues: 343 loop : -1.83 (0.17), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 198 average time/residue: 0.3421 time to fit residues: 109.8307 Evaluate side-chains 173 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2515 time to fit residues: 9.5775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN C 112 GLN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 25525 Z= 0.225 Angle : 0.586 8.495 35762 Z= 0.328 Chirality : 0.040 0.185 4040 Planarity : 0.004 0.061 3532 Dihedral : 26.425 171.185 5460 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.17), residues: 2266 helix: 0.05 (0.19), residues: 738 sheet: -1.09 (0.27), residues: 340 loop : -1.77 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 183 average time/residue: 0.3851 time to fit residues: 114.3142 Evaluate side-chains 163 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2219 time to fit residues: 6.2255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 136 optimal weight: 0.4980 chunk 242 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 148 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 112 GLN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 25525 Z= 0.201 Angle : 0.577 8.510 35762 Z= 0.322 Chirality : 0.039 0.183 4040 Planarity : 0.004 0.063 3532 Dihedral : 26.344 169.237 5460 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2266 helix: 0.26 (0.19), residues: 738 sheet: -1.04 (0.27), residues: 340 loop : -1.76 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 173 average time/residue: 0.3792 time to fit residues: 103.7590 Evaluate side-chains 163 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2205 time to fit residues: 8.0304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 165 optimal weight: 0.0770 chunk 120 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 25525 Z= 0.355 Angle : 0.662 13.665 35762 Z= 0.361 Chirality : 0.043 0.213 4040 Planarity : 0.004 0.064 3532 Dihedral : 26.623 164.461 5460 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2266 helix: -0.12 (0.19), residues: 752 sheet: -1.22 (0.27), residues: 353 loop : -1.83 (0.17), residues: 1161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 178 average time/residue: 0.3551 time to fit residues: 102.4468 Evaluate side-chains 166 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2748 time to fit residues: 9.9146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 8.9990 chunk 212 optimal weight: 0.3980 chunk 226 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 chunk 214 optimal weight: 30.0000 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** M 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN L 95 HIS L 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 25525 Z= 0.164 Angle : 0.585 15.211 35762 Z= 0.322 Chirality : 0.039 0.182 4040 Planarity : 0.004 0.064 3532 Dihedral : 26.296 162.323 5460 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2266 helix: 0.50 (0.20), residues: 737 sheet: -1.13 (0.27), residues: 359 loop : -1.71 (0.17), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 173 average time/residue: 0.3544 time to fit residues: 100.0655 Evaluate side-chains 153 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2150 time to fit residues: 4.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 231 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN K 73 ASN ** M 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 852 GLN ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 ASN L 295 ASN L 325 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.062 25525 Z= 0.486 Angle : 0.740 13.579 35762 Z= 0.401 Chirality : 0.046 0.203 4040 Planarity : 0.005 0.064 3532 Dihedral : 26.825 160.660 5460 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2266 helix: -0.22 (0.19), residues: 747 sheet: -1.18 (0.27), residues: 345 loop : -1.93 (0.17), residues: 1174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 162 average time/residue: 0.3493 time to fit residues: 92.6984 Evaluate side-chains 152 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2209 time to fit residues: 6.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** M 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.097719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068255 restraints weight = 94341.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069192 restraints weight = 53086.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069858 restraints weight = 35064.136| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 25525 Z= 0.206 Angle : 0.614 13.863 35762 Z= 0.337 Chirality : 0.040 0.181 4040 Planarity : 0.004 0.050 3532 Dihedral : 26.563 158.486 5460 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2266 helix: 0.25 (0.19), residues: 753 sheet: -1.29 (0.26), residues: 378 loop : -1.76 (0.17), residues: 1135 =============================================================================== Job complete usr+sys time: 3914.42 seconds wall clock time: 73 minutes 9.32 seconds (4389.32 seconds total)