Starting phenix.real_space_refine on Wed Dec 13 09:30:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/12_2023/6uh5_20767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/12_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_20767/12_2023/6uh5_20767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/12_2023/6uh5_20767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/12_2023/6uh5_20767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uh5_20767/12_2023/6uh5_20767_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.21, per 1000 atoms: 0.50 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: 11.45 Conformation dependent library (CDL) restraints added in 3.4 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: 12.81 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: 10.00 Time building geometry restraints manager: 12.24 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: 12941 35.43 - 70.87: 1637 70.87 - 106.30: 40 106.30 - 141.74: 1 141.74 - 177.17: 2 Dihedral angle restraints: 14621 sinusoidal: 7864 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 14618 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: 1.760 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: 8.170 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 78.680 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.090 ------------------------------------------------------------------------------- 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 : 23.785 177.172 10248 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 % Allowed : 11.61 % Favored : 86.16 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP N 95 HIS 0.018 0.003 HIS K 68 PHE 0.033 0.003 PHE L 153 TYR 0.036 0.004 TYR H 34 ARG 0.015 0.002 ARG G 71 *********************** 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 : 2.524 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: 0.4300 time to fit residues: 193.8380 Evaluate side-chains 161 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2059 time to fit residues: 6.7857 ------------------------------------------------------------------------------- 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 ** 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25525 Z= 0.237 Angle : 0.677 8.267 35762 Z= 0.380 Chirality : 0.043 0.176 4040 Planarity : 0.005 0.069 3532 Dihedral : 27.027 178.107 5748 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 2.38 % Allowed : 15.92 % Favored : 81.70 % 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: -3.42 (0.15), residues: 2266 helix: -2.08 (0.16), residues: 747 sheet: -2.20 (0.23), residues: 381 loop : -2.39 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 348 HIS 0.012 0.001 HIS Q 68 PHE 0.015 0.002 PHE L 25 TYR 0.021 0.001 TYR M 972 ARG 0.008 0.001 ARG E 49 *********************** 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 234 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 228 average time/residue: 0.3714 time to fit residues: 133.0204 Evaluate side-chains 166 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2307 time to fit residues: 10.8156 ------------------------------------------------------------------------------- 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: 0.4980 chunk 190 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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** M 743 ASN ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 ASN L 325 HIS P 94 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25525 Z= 0.297 Angle : 0.652 8.125 35762 Z= 0.363 Chirality : 0.042 0.189 4040 Planarity : 0.005 0.079 3532 Dihedral : 26.672 173.215 5748 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 2.48 % Allowed : 18.11 % Favored : 79.41 % 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: -2.76 (0.16), residues: 2266 helix: -1.32 (0.17), residues: 749 sheet: -1.88 (0.25), residues: 355 loop : -2.15 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 328 HIS 0.007 0.001 HIS L 325 PHE 0.018 0.001 PHE O 121 TYR 0.020 0.002 TYR G 57 ARG 0.022 0.001 ARG P 89 *********************** 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 223 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 214 average time/residue: 0.3460 time to fit residues: 120.9979 Evaluate side-chains 172 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.544 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2175 time to fit residues: 13.4221 ------------------------------------------------------------------------------- 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: 5.9990 chunk 172 optimal weight: 9.9990 chunk 118 optimal weight: 0.0270 chunk 25 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.0242 ------------------------------------------------------------------------------- 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** M 852 GLN ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25525 Z= 0.187 Angle : 0.594 10.041 35762 Z= 0.332 Chirality : 0.040 0.172 4040 Planarity : 0.004 0.062 3532 Dihedral : 26.352 175.049 5748 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 1.74 % Allowed : 19.25 % Favored : 79.02 % 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: -2.18 (0.17), residues: 2266 helix: -0.63 (0.19), residues: 740 sheet: -1.54 (0.26), residues: 343 loop : -1.96 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 348 HIS 0.008 0.001 HIS L 325 PHE 0.014 0.001 PHE L 293 TYR 0.022 0.001 TYR G 57 ARG 0.006 0.000 ARG K 325 *********************** 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 210 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 201 average time/residue: 0.3628 time to fit residues: 117.0983 Evaluate side-chains 176 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2243 time to fit residues: 11.3574 ------------------------------------------------------------------------------- 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: 9.9990 chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** K 138 HIS M 743 ASN ** N 258 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: 0.7918 moved from start: 0.3438 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= 0.236 Angle : 0.599 8.779 35762 Z= 0.334 Chirality : 0.040 0.223 4040 Planarity : 0.004 0.054 3532 Dihedral : 26.263 172.869 5748 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 1.93 % Allowed : 19.15 % Favored : 78.92 % 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: -1.95 (0.17), residues: 2266 helix: -0.37 (0.19), residues: 751 sheet: -1.40 (0.27), residues: 343 loop : -1.89 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 95 HIS 0.008 0.001 HIS L 325 PHE 0.021 0.001 PHE X 327 TYR 0.024 0.001 TYR G 57 ARG 0.005 0.000 ARG M 903 *********************** 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 207 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 168 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 200 average time/residue: 0.3710 time to fit residues: 119.3909 Evaluate side-chains 176 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2559 time to fit residues: 10.8321 ------------------------------------------------------------------------------- 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: 4.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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: 0.7883 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25525 Z= 0.181 Angle : 0.575 8.633 35762 Z= 0.322 Chirality : 0.039 0.190 4040 Planarity : 0.004 0.060 3532 Dihedral : 26.073 171.721 5748 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.19 % Allowed : 19.84 % Favored : 78.97 % 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: -1.64 (0.17), residues: 2266 helix: 0.01 (0.19), residues: 746 sheet: -1.31 (0.26), residues: 347 loop : -1.76 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 348 HIS 0.009 0.001 HIS L 325 PHE 0.017 0.001 PHE N 10 TYR 0.024 0.001 TYR P 90 ARG 0.004 0.000 ARG M 903 *********************** 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 194 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 190 average time/residue: 0.3639 time to fit residues: 112.4146 Evaluate side-chains 168 residues out of total 2036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2277 time to fit residues: 8.5548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2234 > 50: distance: 52 - 57: 28.170 distance: 57 - 58: 25.262 distance: 58 - 59: 60.833 distance: 58 - 61: 20.528 distance: 59 - 60: 52.961 distance: 59 - 65: 40.246 distance: 60 - 87: 18.972 distance: 61 - 62: 7.003 distance: 62 - 63: 35.333 distance: 62 - 64: 40.574 distance: 65 - 66: 69.131 distance: 66 - 67: 41.309 distance: 66 - 69: 56.541 distance: 67 - 73: 23.797 distance: 69 - 70: 37.430 distance: 70 - 71: 40.089 distance: 70 - 72: 17.398 distance: 73 - 74: 25.317 distance: 74 - 75: 34.002 distance: 74 - 77: 14.915 distance: 75 - 76: 20.359 distance: 75 - 81: 48.378 distance: 77 - 78: 57.855 distance: 77 - 79: 48.238 distance: 78 - 80: 55.809 distance: 81 - 82: 40.477 distance: 82 - 83: 36.818 distance: 82 - 85: 38.530 distance: 83 - 84: 3.733 distance: 83 - 87: 35.392 distance: 85 - 86: 50.851 distance: 87 - 88: 40.067 distance: 88 - 89: 20.137 distance: 88 - 91: 20.626 distance: 89 - 90: 20.491 distance: 89 - 94: 44.771 distance: 91 - 92: 18.678 distance: 91 - 93: 19.605 distance: 94 - 95: 32.164 distance: 95 - 96: 8.436 distance: 95 - 98: 9.339 distance: 96 - 97: 23.345 distance: 96 - 105: 56.746 distance: 97 - 129: 51.744 distance: 98 - 99: 28.124 distance: 99 - 100: 29.706 distance: 100 - 101: 13.948 distance: 101 - 102: 10.189 distance: 102 - 103: 6.875 distance: 102 - 104: 18.884 distance: 105 - 106: 21.916 distance: 106 - 107: 23.341 distance: 106 - 109: 10.970 distance: 107 - 108: 21.442 distance: 107 - 112: 31.926 distance: 108 - 137: 36.034 distance: 109 - 110: 26.228 distance: 109 - 111: 31.550 distance: 112 - 113: 21.373 distance: 113 - 114: 40.079 distance: 113 - 116: 31.115 distance: 114 - 115: 36.238 distance: 114 - 120: 40.721 distance: 116 - 117: 38.838 distance: 117 - 119: 20.787 distance: 120 - 121: 34.380 distance: 121 - 122: 52.417 distance: 121 - 124: 32.121 distance: 122 - 123: 10.752 distance: 122 - 129: 16.024 distance: 124 - 125: 30.175 distance: 125 - 126: 46.733 distance: 126 - 127: 16.380 distance: 126 - 128: 40.335 distance: 129 - 130: 49.883 distance: 130 - 131: 31.493 distance: 130 - 133: 22.324 distance: 131 - 132: 15.151 distance: 131 - 137: 28.967 distance: 133 - 134: 65.737 distance: 134 - 135: 5.852 distance: 134 - 136: 6.702