Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 21:34:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/07_2023/6qld_4579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/07_2023/6qld_4579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/07_2023/6qld_4579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/07_2023/6qld_4579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/07_2023/6qld_4579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/07_2023/6qld_4579.pdb" } resolution = 4.15 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 86 5.16 5 C 17735 2.51 5 N 5188 2.21 5 O 5829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 299": "NH1" <-> "NH2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "I ASP 389": "OD1" <-> "OD2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I ASP 517": "OD1" <-> "OD2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ARG 119": "NH1" <-> "NH2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L ASP 186": "OD1" <-> "OD2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "N ASP 135": "OD1" <-> "OD2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 182": "OD1" <-> "OD2" Residue "O ASP 198": "OD1" <-> "OD2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O GLU 277": "OE1" <-> "OE2" Residue "O ASP 296": "OD1" <-> "OD2" Residue "O ASP 298": "OD1" <-> "OD2" Residue "O GLU 323": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 173": "OD1" <-> "OD2" Residue "P TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 246": "OE1" <-> "OE2" Residue "P TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 264": "NH1" <-> "NH2" Residue "Q ASP 338": "OD1" <-> "OD2" Residue "Q ASP 345": "OD1" <-> "OD2" Residue "U PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 187": "NH1" <-> "NH2" Residue "U ARG 212": "NH1" <-> "NH2" Residue "U ASP 248": "OD1" <-> "OD2" Residue "U ASP 286": "OD1" <-> "OD2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 109": "OD1" <-> "OD2" Residue "a GLU 188": "OE1" <-> "OE2" Residue "b ASP 69": "OD1" <-> "OD2" Residue "f ASP 69": "OD1" <-> "OD2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "f ASP 86": "OD1" <-> "OD2" Residue "g TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 80": "OE1" <-> "OE2" Residue "i ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 29086 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 194 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "G" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2524 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 948 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "I" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2701 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 175 Chain: "J" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2560 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "K" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 774 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "L" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1937 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2929 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 71 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1865 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "Q" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1421 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 156 Chain: "U" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1229 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "a" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 706 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 719 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 45 Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 788 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Time building chain proxies: 13.83, per 1000 atoms: 0.48 Number of scatterers: 29086 At special positions: 0 Unit cell: (183.12, 226.72, 135.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 248 15.00 O 5829 8.00 N 5188 7.00 C 17735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.01 Conformation dependent library (CDL) restraints added in 3.7 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6076 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 15 sheets defined 64.2% alpha, 6.6% beta 120 base pairs and 204 stacking pairs defined. Time for finding SS restraints: 9.15 Creating SS restraints... Processing helix chain 'H' and resid 5 through 38 Processing helix chain 'H' and resid 46 through 73 Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 96 through 135 Processing helix chain 'I' and resid 334 through 338 removed outlier: 4.199A pdb=" N HIS I 338 " --> pdb=" O SER I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 349 removed outlier: 3.553A pdb=" N SER I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 removed outlier: 3.505A pdb=" N GLU I 358 " --> pdb=" O SER I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 399 Processing helix chain 'I' and resid 402 through 407 Processing helix chain 'I' and resid 409 through 421 Processing helix chain 'I' and resid 432 through 450 Processing helix chain 'I' and resid 457 through 473 removed outlier: 4.125A pdb=" N THR I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 493 Processing helix chain 'I' and resid 506 through 524 Processing helix chain 'I' and resid 538 through 548 Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 577 through 592 Processing helix chain 'I' and resid 607 through 619 removed outlier: 3.521A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 651 Processing helix chain 'I' and resid 666 through 675 Processing helix chain 'I' and resid 695 through 707 removed outlier: 3.776A pdb=" N THR I 707 " --> pdb=" O HIS I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 721 Processing helix chain 'I' and resid 722 through 726 removed outlier: 3.508A pdb=" N SER I 726 " --> pdb=" O LYS I 723 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 40 Processing helix chain 'K' and resid 51 through 58 Processing helix chain 'K' and resid 70 through 127 Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 94 through 106 Processing helix chain 'L' and resid 118 through 128 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.618A pdb=" N ASP L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 196 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.609A pdb=" N LEU L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 3.827A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.530A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 64 removed outlier: 3.868A pdb=" N LEU N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 77 removed outlier: 3.924A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 124 through 137 removed outlier: 3.624A pdb=" N PHE N 128 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE N 129 " --> pdb=" O PRO N 125 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 232 Processing helix chain 'N' and resid 250 through 259 Processing helix chain 'N' and resid 261 through 265 removed outlier: 4.492A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 273 removed outlier: 4.397A pdb=" N CYS N 272 " --> pdb=" O PRO N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 423 through 427 removed outlier: 3.598A pdb=" N VAL N 427 " --> pdb=" O ILE N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 433 removed outlier: 3.661A pdb=" N GLY N 433 " --> pdb=" O GLY N 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 246 through 253 Processing helix chain 'O' and resid 254 through 257 removed outlier: 3.813A pdb=" N LEU O 257 " --> pdb=" O ASN O 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 254 through 257' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.583A pdb=" N ALA O 264 " --> pdb=" O SER O 260 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 348 removed outlier: 3.591A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 363 removed outlier: 3.607A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS O 361 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER O 362 " --> pdb=" O LYS O 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 110 Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.880A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 224 through 232 removed outlier: 4.262A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 266 Processing helix chain 'P' and resid 333 through 348 removed outlier: 4.017A pdb=" N LEU P 337 " --> pdb=" O ASN P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 363 Processing helix chain 'Q' and resid 162 through 184 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 3.657A pdb=" N LEU Q 206 " --> pdb=" O LYS Q 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 207 " --> pdb=" O LYS Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 293 Processing helix chain 'Q' and resid 322 through 333 Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.032A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 391 removed outlier: 3.829A pdb=" N PHE Q 390 " --> pdb=" O ILE Q 386 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL Q 391 " --> pdb=" O LYS Q 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 155 Proline residue: U 152 - end of helix Processing helix chain 'U' and resid 167 through 231 removed outlier: 3.594A pdb=" N LYS U 172 " --> pdb=" O LYS U 168 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 173 " --> pdb=" O LEU U 169 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU U 175 " --> pdb=" O TYR U 171 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.848A pdb=" N LEU U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 318 removed outlier: 3.845A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.700A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 22 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 57 through 83 removed outlier: 3.880A pdb=" N SER Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 103 removed outlier: 3.871A pdb=" N ARG Y 98 " --> pdb=" O GLY Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 118 removed outlier: 3.567A pdb=" N LEU Y 118 " --> pdb=" O ILE Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 186 Processing helix chain 'Y' and resid 189 through 196 Processing helix chain 'Y' and resid 196 through 219 removed outlier: 3.695A pdb=" N PHE Y 219 " --> pdb=" O ALA Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 238 removed outlier: 4.343A pdb=" N LYS Y 238 " --> pdb=" O SER Y 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 14 removed outlier: 3.549A pdb=" N ASN Z 9 " --> pdb=" O GLN Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 23 removed outlier: 3.609A pdb=" N PHE Z 22 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 43 Processing helix chain 'Z' and resid 43 through 82 removed outlier: 3.918A pdb=" N ALA Z 48 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR Z 54 " --> pdb=" O ASP Z 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG Z 71 " --> pdb=" O THR Z 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER Z 78 " --> pdb=" O ARG Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 124 removed outlier: 3.745A pdb=" N ASN Z 124 " --> pdb=" O ALA Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 152 removed outlier: 4.221A pdb=" N ALA Z 135 " --> pdb=" O ALA Z 131 " (cutoff:3.500A) Proline residue: Z 137 - end of helix Processing helix chain 'a' and resid 138 through 146 removed outlier: 4.316A pdb=" N ILE a 142 " --> pdb=" O ALA a 138 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN a 146 " --> pdb=" O ILE a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 170 Processing helix chain 'a' and resid 179 through 208 removed outlier: 4.343A pdb=" N LEU a 203 " --> pdb=" O GLU a 199 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU a 204 " --> pdb=" O HIS a 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU a 206 " --> pdb=" O ASN a 202 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA a 208 " --> pdb=" O LEU a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 221 Processing helix chain 'a' and resid 222 through 225 Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 49 through 77 removed outlier: 4.485A pdb=" N GLU b 53 " --> pdb=" O GLY b 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL b 66 " --> pdb=" O PHE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 95 Processing helix chain 'd' and resid 41 through 53 removed outlier: 3.509A pdb=" N GLN d 51 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR d 52 " --> pdb=" O VAL d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 88 removed outlier: 3.643A pdb=" N MET d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 106 removed outlier: 3.839A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 128 Processing helix chain 'e' and resid 113 through 128 Processing helix chain 'e' and resid 139 through 146 removed outlier: 4.148A pdb=" N ARG e 143 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 167 Processing helix chain 'e' and resid 179 through 208 removed outlier: 3.503A pdb=" N ILE e 183 " --> pdb=" O GLN e 179 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU e 203 " --> pdb=" O GLU e 199 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU e 204 " --> pdb=" O HIS e 200 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 224 removed outlier: 3.917A pdb=" N LEU e 220 " --> pdb=" O LYS e 216 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA e 221 " --> pdb=" O ASP e 217 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARG e 222 " --> pdb=" O MET e 218 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 30 removed outlier: 4.336A pdb=" N ILE f 30 " --> pdb=" O ILE f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 42 Processing helix chain 'f' and resid 50 through 77 removed outlier: 4.299A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP f 69 " --> pdb=" O SER f 65 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR f 74 " --> pdb=" O SER f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 94 Processing helix chain 'g' and resid 28 through 40 removed outlier: 4.217A pdb=" N VAL g 32 " --> pdb=" O PRO g 28 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN g 40 " --> pdb=" O LEU g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 75 removed outlier: 4.381A pdb=" N VAL g 51 " --> pdb=" O SER g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 90 Processing helix chain 'g' and resid 92 through 99 Processing helix chain 'h' and resid 41 through 53 Processing helix chain 'h' and resid 59 through 88 Processing helix chain 'h' and resid 94 through 106 removed outlier: 4.026A pdb=" N ILE h 98 " --> pdb=" O SER h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 126 Processing helix chain 'i' and resid 28 through 38 Processing helix chain 'i' and resid 48 through 74 removed outlier: 3.818A pdb=" N TYR i 52 " --> pdb=" O GLY i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 91 removed outlier: 3.523A pdb=" N ASN i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 100 Processing sheet with id=AA1, first strand: chain 'L' and resid 73 through 76 removed outlier: 3.533A pdb=" N PHE L 86 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR L 3 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR L 223 " --> pdb=" O TYR L 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 33 through 36 removed outlier: 4.221A pdb=" N ASP L 34 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU L 57 " --> pdb=" O ASP L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'L' and resid 162 through 164 Processing sheet with id=AA5, first strand: chain 'N' and resid 106 through 110 removed outlier: 7.208A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 106 through 110 removed outlier: 7.208A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 112 through 113 removed outlier: 3.505A pdb=" N ARG N 113 " --> pdb=" O LYS N 117 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 117 " --> pdb=" O ARG N 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'O' and resid 175 through 180 removed outlier: 3.928A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 305 through 309 removed outlier: 6.028A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY O 350 " --> pdb=" O ILE O 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 165 through 175 removed outlier: 5.669A pdb=" N VAL P 167 " --> pdb=" O LYS P 188 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS P 188 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL P 169 " --> pdb=" O ASN P 186 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN P 186 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER P 171 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 180 " --> pdb=" O VAL P 175 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU P 181 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS P 214 " --> pdb=" O PHE P 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 270 through 273 removed outlier: 3.769A pdb=" N ARG P 270 " --> pdb=" O GLU P 283 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU P 283 " --> pdb=" O ARG P 270 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET P 318 " --> pdb=" O THR P 303 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER P 319 " --> pdb=" O MET Q 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 97 through 99 removed outlier: 6.314A pdb=" N THR b 97 " --> pdb=" O THR g 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'd' and resid 57 through 58 removed outlier: 7.501A pdb=" N GLY d 57 " --> pdb=" O ILE i 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'd' and resid 92 through 93 Processing sheet with id=AB6, first strand: chain 'e' and resid 177 through 178 removed outlier: 7.453A pdb=" N ARG e 177 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 1560 hydrogen bonds defined for protein. 4617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 204 stacking parallelities Total time for adding SS restraints: 13.48 Time building geometry restraints manager: 12.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7413 1.34 - 1.46: 6957 1.46 - 1.58: 15030 1.58 - 1.70: 492 1.70 - 1.82: 145 Bond restraints: 30037 Sorted by residual: bond pdb=" O3' DG G 4 " pdb=" P DA G 5 " ideal model delta sigma weight residual 1.607 1.458 0.149 1.50e-02 4.44e+03 9.83e+01 bond pdb=" O3' DT J -5 " pdb=" P DC J -4 " ideal model delta sigma weight residual 1.607 1.534 0.073 1.50e-02 4.44e+03 2.35e+01 bond pdb=" N VAL L 40 " pdb=" CA VAL L 40 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 9.09e+00 bond pdb=" N ARG I 350 " pdb=" CA ARG I 350 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.58e+00 bond pdb=" N SER I 349 " pdb=" CA SER I 349 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.35e-02 5.49e+03 6.39e+00 ... (remaining 30032 not shown) Histogram of bond angle deviations from ideal: 75.11 - 86.92: 1 86.92 - 98.72: 7 98.72 - 110.53: 10092 110.53 - 122.33: 27171 122.33 - 134.14: 4421 Bond angle restraints: 41692 Sorted by residual: angle pdb=" O3' DG G 4 " pdb=" P DA G 5 " pdb=" O5' DA G 5 " ideal model delta sigma weight residual 104.00 121.03 -17.03 1.50e+00 4.44e-01 1.29e+02 angle pdb=" O3' DG G 4 " pdb=" P DA G 5 " pdb=" OP1 DA G 5 " ideal model delta sigma weight residual 108.00 75.11 32.89 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C3' DT J -5 " pdb=" O3' DT J -5 " pdb=" P DC J -4 " ideal model delta sigma weight residual 120.20 106.66 13.54 1.50e+00 4.44e-01 8.14e+01 angle pdb=" O3' DT J -5 " pdb=" P DC J -4 " pdb=" O5' DC J -4 " ideal model delta sigma weight residual 104.00 90.89 13.11 1.50e+00 4.44e-01 7.64e+01 angle pdb=" O3' DG J -3 " pdb=" C3' DG J -3 " pdb=" C2' DG J -3 " ideal model delta sigma weight residual 111.50 99.86 11.64 1.50e+00 4.44e-01 6.02e+01 ... (remaining 41687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 15867 34.88 - 69.76: 1430 69.76 - 104.64: 38 104.64 - 139.52: 2 139.52 - 174.40: 1 Dihedral angle restraints: 17338 sinusoidal: 8058 harmonic: 9280 Sorted by residual: dihedral pdb=" CA MET P 274 " pdb=" C MET P 274 " pdb=" N ASN P 275 " pdb=" CA ASN P 275 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR N 77 " pdb=" C TYR N 77 " pdb=" N VAL N 78 " pdb=" CA VAL N 78 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER N 266 " pdb=" C SER N 266 " pdb=" N MET N 267 " pdb=" CA MET N 267 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 17335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4153 0.061 - 0.122: 682 0.122 - 0.183: 106 0.183 - 0.244: 6 0.244 - 0.305: 2 Chirality restraints: 4949 Sorted by residual: chirality pdb=" CA PRO L 41 " pdb=" N PRO L 41 " pdb=" C PRO L 41 " pdb=" CB PRO L 41 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ASP I 334 " pdb=" N ASP I 334 " pdb=" C ASP I 334 " pdb=" CB ASP I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE a 224 " pdb=" CA ILE a 224 " pdb=" CG1 ILE a 224 " pdb=" CG2 ILE a 224 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4946 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 40 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C VAL L 40 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL L 40 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO L 41 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 297 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.83e+00 pdb=" C TYR C 297 " 0.054 2.00e-02 2.50e+03 pdb=" O TYR C 297 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP C 298 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 39 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C ARG L 39 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG L 39 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL L 40 " -0.018 2.00e-02 2.50e+03 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7901 2.81 - 3.33: 25779 3.33 - 3.86: 51607 3.86 - 4.38: 54837 4.38 - 4.90: 89113 Nonbonded interactions: 229237 Sorted by model distance: nonbonded pdb=" OP1 DG G 102 " pdb=" N LYS f 80 " model vdw 2.289 2.520 nonbonded pdb=" O LEU I 701 " pdb=" OG SER I 705 " model vdw 2.294 2.440 nonbonded pdb=" OP2 DT G 31 " pdb=" NH2 ARG i 19 " model vdw 2.302 2.520 nonbonded pdb=" OG SER d 59 " pdb=" OG SER d 62 " model vdw 2.314 2.440 nonbonded pdb=" O SER O 214 " pdb=" OG SER O 214 " model vdw 2.315 2.440 ... (remaining 229232 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 'b' selection = (chain 'f' and (resid 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 103)) } ncs_group { reference = chain 'd' selection = (chain 'h' and (resid 37 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 129)) } ncs_group { reference = (chain 'g' and resid 17 through 118) selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 9.660 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 79.460 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.170 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.004 0.149 30037 Z= 0.256 Angle : 0.856 32.888 41692 Z= 0.491 Chirality : 0.047 0.305 4949 Planarity : 0.005 0.062 4371 Dihedral : 21.511 174.403 11262 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.12), residues: 3051 helix: -1.89 (0.09), residues: 1896 sheet: -2.43 (0.32), residues: 234 loop : -2.90 (0.17), residues: 921 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 664 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 669 average time/residue: 0.4867 time to fit residues: 487.9690 Evaluate side-chains 383 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 2.987 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2444 time to fit residues: 4.5642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 301 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN H 88 ASN H 113 GLN I 348 ASN I 376 GLN I 487 HIS I 582 ASN I 590 ASN I 613 GLN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN K 111 ASN L 78 ASN L 131 HIS N 133 GLN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 423 ASN ** O 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN P 223 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 255 ASN ** Q 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 217 ASN U 237 HIS U 310 ASN Y 158 GLN Z 47 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN ** a 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 202 ASN d 53 HIS ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 91 ASN g 115 GLN h 67 ASN i 116 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 30037 Z= 0.248 Angle : 0.616 10.321 41692 Z= 0.337 Chirality : 0.038 0.243 4949 Planarity : 0.005 0.143 4371 Dihedral : 23.743 174.039 5849 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.66 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3051 helix: 0.25 (0.11), residues: 1930 sheet: -1.83 (0.34), residues: 235 loop : -2.55 (0.19), residues: 886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 503 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 505 average time/residue: 0.4307 time to fit residues: 336.2686 Evaluate side-chains 362 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 3.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 250 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 326 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 242 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 HIS I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN K 111 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 253 ASN ** O 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 GLN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 HIS e 174 GLN ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 GLN h 67 ASN i 114 HIS i 116 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 30037 Z= 0.295 Angle : 0.642 9.842 41692 Z= 0.348 Chirality : 0.039 0.191 4949 Planarity : 0.005 0.136 4371 Dihedral : 23.898 174.082 5849 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 3051 helix: 1.05 (0.12), residues: 1935 sheet: -1.63 (0.35), residues: 231 loop : -2.28 (0.20), residues: 885 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 467 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 469 average time/residue: 0.4399 time to fit residues: 321.8496 Evaluate side-chains 342 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 3.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2524 time to fit residues: 4.6439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 202 optimal weight: 0.4980 chunk 303 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS I 363 GLN I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 423 ASN O 168 ASN P 160 HIS P 259 GLN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 HIS e 207 HIS f 94 GLN ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN h 71 ASN i 116 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30037 Z= 0.190 Angle : 0.578 13.128 41692 Z= 0.311 Chirality : 0.038 0.192 4949 Planarity : 0.004 0.157 4371 Dihedral : 23.868 173.267 5849 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.89 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 3051 helix: 1.50 (0.12), residues: 1933 sheet: -1.31 (0.36), residues: 229 loop : -2.13 (0.21), residues: 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 481 average time/residue: 0.4221 time to fit residues: 317.8508 Evaluate side-chains 350 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 349 time to evaluate : 2.990 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2979 time to fit residues: 4.4091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 363 GLN I 487 HIS ** I 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 95 HIS ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 GLN ** Y 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN i 114 HIS i 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 30037 Z= 0.402 Angle : 0.717 10.168 41692 Z= 0.383 Chirality : 0.042 0.184 4949 Planarity : 0.005 0.138 4371 Dihedral : 24.076 173.206 5849 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.51 % Favored : 92.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 3051 helix: 1.33 (0.12), residues: 1922 sheet: -1.62 (0.35), residues: 233 loop : -2.16 (0.21), residues: 896 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.4173 time to fit residues: 282.1269 Evaluate side-chains 315 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 HIS I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 253 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Z 8 HIS ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 113 HIS ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN i 114 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 30037 Z= 0.249 Angle : 0.619 11.027 41692 Z= 0.336 Chirality : 0.039 0.168 4949 Planarity : 0.004 0.130 4371 Dihedral : 24.072 172.668 5849 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 3051 helix: 1.52 (0.12), residues: 1924 sheet: -1.22 (0.38), residues: 217 loop : -2.06 (0.21), residues: 910 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 443 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 445 average time/residue: 0.4207 time to fit residues: 300.7227 Evaluate side-chains 322 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 320 time to evaluate : 2.916 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3351 time to fit residues: 4.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 8.9990 chunk 36 optimal weight: 0.0870 chunk 183 optimal weight: 0.1980 chunk 234 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 319 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 423 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 219 GLN ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS e 207 HIS f 94 GLN g 33 HIS ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN i 33 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 30037 Z= 0.163 Angle : 0.587 12.235 41692 Z= 0.315 Chirality : 0.038 0.216 4949 Planarity : 0.004 0.149 4371 Dihedral : 23.913 172.940 5849 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 3051 helix: 1.79 (0.12), residues: 1937 sheet: -0.95 (0.38), residues: 221 loop : -1.97 (0.21), residues: 893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.4211 time to fit residues: 307.5571 Evaluate side-chains 339 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 96 optimal weight: 0.0980 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 251 optimal weight: 3.9990 overall best weight: 1.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 HIS ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30037 Z= 0.219 Angle : 0.613 11.476 41692 Z= 0.330 Chirality : 0.039 0.230 4949 Planarity : 0.004 0.137 4371 Dihedral : 23.915 173.506 5849 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 3051 helix: 1.83 (0.12), residues: 1936 sheet: -0.89 (0.38), residues: 224 loop : -1.94 (0.21), residues: 891 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.4036 time to fit residues: 283.7611 Evaluate side-chains 324 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 HIS ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30037 Z= 0.214 Angle : 0.614 11.539 41692 Z= 0.330 Chirality : 0.039 0.219 4949 Planarity : 0.004 0.131 4371 Dihedral : 23.897 173.378 5849 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 3051 helix: 1.89 (0.12), residues: 1932 sheet: -0.85 (0.38), residues: 224 loop : -1.86 (0.21), residues: 895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.4058 time to fit residues: 278.2760 Evaluate side-chains 318 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 330 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN L 238 GLN ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 HIS ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 HIS ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 HIS h 67 ASN ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 30037 Z= 0.335 Angle : 0.696 11.247 41692 Z= 0.372 Chirality : 0.041 0.189 4949 Planarity : 0.005 0.131 4371 Dihedral : 24.045 173.347 5849 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 3051 helix: 1.63 (0.12), residues: 1925 sheet: -1.15 (0.37), residues: 228 loop : -1.95 (0.21), residues: 898 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.4032 time to fit residues: 262.4127 Evaluate side-chains 303 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 3.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 423 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 HIS ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 GLN ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.085707 restraints weight = 108062.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.086769 restraints weight = 192726.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087493 restraints weight = 102159.317| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 30037 Z= 0.280 Angle : 0.662 11.451 41692 Z= 0.355 Chirality : 0.040 0.179 4949 Planarity : 0.004 0.130 4371 Dihedral : 24.061 173.019 5849 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 3051 helix: 1.64 (0.12), residues: 1925 sheet: -1.11 (0.38), residues: 226 loop : -1.90 (0.21), residues: 900 =============================================================================== Job complete usr+sys time: 5767.50 seconds wall clock time: 105 minutes 48.25 seconds (6348.25 seconds total)