Starting phenix.real_space_refine on Thu Mar 21 03:26:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/03_2024/6qld_4579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/03_2024/6qld_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_4579/03_2024/6qld_4579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/03_2024/6qld_4579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/03_2024/6qld_4579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qld_4579/03_2024/6qld_4579.pdb" } resolution = 4.15 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= 0.003 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-dev-5265/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: 15.49, per 1000 atoms: 0.53 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: 12.98 Conformation dependent library (CDL) restraints added in 4.5 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: 10.29 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: 11.95 Time building geometry restraints manager: 13.82 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: 16019 34.88 - 69.76: 1478 69.76 - 104.64: 38 104.64 - 139.52: 2 139.52 - 174.40: 1 Dihedral angle restraints: 17538 sinusoidal: 8258 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 17535 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 8.270 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 83.330 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.130 ------------------------------------------------------------------------------- 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 : 21.698 174.403 11462 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 % Allowed : 8.17 % Favored : 91.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 472 HIS 0.006 0.001 HIS O 238 PHE 0.021 0.002 PHE I 719 TYR 0.017 0.002 TYR O 170 ARG 0.004 0.000 ARG P 174 *********************** 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 : 3.330 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: H 55 ILE cc_start: 0.9354 (mt) cc_final: 0.9122 (mt) REVERT: H 56 ARG cc_start: 0.8418 (ttp80) cc_final: 0.7787 (ttt180) REVERT: H 65 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8315 (tmtt) REVERT: I 346 ILE cc_start: 0.7852 (pt) cc_final: 0.7542 (tp) REVERT: I 364 LEU cc_start: 0.9377 (tp) cc_final: 0.8956 (mm) REVERT: I 512 PHE cc_start: 0.8359 (t80) cc_final: 0.8034 (t80) REVERT: I 516 LEU cc_start: 0.8944 (mt) cc_final: 0.8662 (tp) REVERT: I 612 LYS cc_start: 0.8500 (mttt) cc_final: 0.7989 (tptp) REVERT: K 22 LYS cc_start: 0.8455 (mttt) cc_final: 0.8075 (mmtt) REVERT: K 108 ASN cc_start: 0.7964 (m-40) cc_final: 0.7385 (p0) REVERT: L 121 MET cc_start: 0.8726 (mtp) cc_final: 0.8113 (mtp) REVERT: L 154 GLN cc_start: 0.8028 (mt0) cc_final: 0.7713 (tt0) REVERT: L 185 ASN cc_start: 0.7980 (t0) cc_final: 0.7471 (t0) REVERT: L 217 MET cc_start: 0.8167 (mtt) cc_final: 0.7845 (mtp) REVERT: N 25 MET cc_start: 0.8042 (mmm) cc_final: 0.7738 (tpt) REVERT: N 211 ILE cc_start: 0.8676 (mt) cc_final: 0.8457 (pt) REVERT: N 225 LEU cc_start: 0.9433 (tp) cc_final: 0.9109 (tp) REVERT: N 252 HIS cc_start: 0.7840 (m-70) cc_final: 0.7626 (m-70) REVERT: N 397 ILE cc_start: 0.9416 (mm) cc_final: 0.9039 (mt) REVERT: N 415 GLU cc_start: 0.8783 (tt0) cc_final: 0.8551 (tt0) REVERT: N 443 MET cc_start: 0.7941 (tpt) cc_final: 0.7640 (tpp) REVERT: O 164 ILE cc_start: 0.9521 (mt) cc_final: 0.9243 (mm) REVERT: O 237 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9092 (mmmt) REVERT: O 262 ASP cc_start: 0.7915 (p0) cc_final: 0.6874 (t0) REVERT: O 277 GLU cc_start: 0.8471 (tt0) cc_final: 0.7646 (tm-30) REVERT: O 283 GLN cc_start: 0.9035 (tt0) cc_final: 0.8754 (tm-30) REVERT: O 305 MET cc_start: 0.7768 (ttm) cc_final: 0.7509 (tpp) REVERT: P 143 ASP cc_start: 0.7568 (p0) cc_final: 0.7274 (p0) REVERT: P 348 TYR cc_start: 0.7671 (m-10) cc_final: 0.7443 (m-10) REVERT: Q 251 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7968 (mm-30) REVERT: Q 331 GLU cc_start: 0.8975 (tt0) cc_final: 0.8704 (tt0) REVERT: Q 337 ASN cc_start: 0.8845 (t0) cc_final: 0.8539 (t0) REVERT: U 178 PHE cc_start: 0.7636 (m-80) cc_final: 0.7316 (m-10) REVERT: U 308 LYS cc_start: 0.8950 (mttt) cc_final: 0.8388 (tttt) REVERT: Y 59 GLN cc_start: 0.7636 (pt0) cc_final: 0.7217 (pt0) REVERT: Y 81 ILE cc_start: 0.7953 (tp) cc_final: 0.7729 (tp) REVERT: Y 155 GLN cc_start: 0.8410 (mt0) cc_final: 0.8004 (mt0) REVERT: Y 158 GLN cc_start: 0.8557 (mt0) cc_final: 0.8356 (mt0) REVERT: a 160 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7167 (mtp180) REVERT: a 179 GLN cc_start: 0.7803 (mt0) cc_final: 0.7370 (mp10) REVERT: a 183 ILE cc_start: 0.7404 (mm) cc_final: 0.6939 (tp) REVERT: a 193 TYR cc_start: 0.7986 (t80) cc_final: 0.7755 (t80) REVERT: a 195 VAL cc_start: 0.8452 (p) cc_final: 0.8234 (p) REVERT: b 54 GLU cc_start: 0.8594 (tp30) cc_final: 0.8353 (mt-10) REVERT: d 53 HIS cc_start: 0.7175 (m-70) cc_final: 0.6162 (m-70) REVERT: d 63 MET cc_start: 0.7996 (tpp) cc_final: 0.7595 (tpp) REVERT: d 120 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7001 (ptt90) REVERT: e 163 LYS cc_start: 0.8178 (tttt) cc_final: 0.7395 (mptt) REVERT: e 164 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7289 (tm-30) REVERT: e 187 GLN cc_start: 0.8893 (tt0) cc_final: 0.8398 (tm-30) REVERT: e 223 ARG cc_start: 0.7880 (tmt-80) cc_final: 0.7509 (tpm170) REVERT: f 50 LEU cc_start: 0.8641 (tp) cc_final: 0.8106 (mp) REVERT: f 89 TYR cc_start: 0.8992 (m-10) cc_final: 0.8530 (m-80) REVERT: g 34 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7708 (ptm-80) REVERT: g 90 ARG cc_start: 0.8010 (mmt-90) cc_final: 0.7653 (ptt-90) REVERT: h 75 GLU cc_start: 0.8806 (tp30) cc_final: 0.8008 (tp30) REVERT: h 103 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7135 (ttm-80) REVERT: i 44 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.6628 (mtp85) REVERT: i 58 GLU cc_start: 0.8538 (tt0) cc_final: 0.7839 (tm-30) REVERT: i 104 ILE cc_start: 0.8943 (mm) cc_final: 0.8491 (mt) REVERT: i 114 HIS cc_start: 0.6647 (t-90) cc_final: 0.6306 (t-90) outliers start: 6 outliers final: 2 residues processed: 669 average time/residue: 0.4640 time to fit residues: 462.4595 Evaluate side-chains 419 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 3.000 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 301 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 73 ASN 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** ** O 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN P 223 ASN ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 255 ASN U 217 ASN U 237 HIS U 310 ASN Y 158 GLN Z 47 GLN ** Z 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 202 ASN ** f 26 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: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30037 Z= 0.233 Angle : 0.602 10.243 41692 Z= 0.331 Chirality : 0.038 0.220 4949 Planarity : 0.005 0.143 4371 Dihedral : 23.840 174.162 6049 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % 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: -1.05 (0.15), residues: 3051 helix: 0.29 (0.11), residues: 1937 sheet: -1.76 (0.34), residues: 235 loop : -2.52 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 472 HIS 0.007 0.001 HIS i 33 PHE 0.030 0.002 PHE I 512 TYR 0.020 0.002 TYR f 73 ARG 0.007 0.001 ARG a 210 *********************** 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 520 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 518 time to evaluate : 3.213 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: H 112 LYS cc_start: 0.8565 (mptt) cc_final: 0.8306 (mptt) REVERT: I 364 LEU cc_start: 0.9423 (tp) cc_final: 0.9129 (mm) REVERT: I 459 SER cc_start: 0.8794 (m) cc_final: 0.8541 (m) REVERT: I 546 PHE cc_start: 0.8243 (m-80) cc_final: 0.8027 (m-80) REVERT: I 612 LYS cc_start: 0.8646 (mttt) cc_final: 0.8053 (tptp) REVERT: K 22 LYS cc_start: 0.8463 (mttt) cc_final: 0.8115 (ptpt) REVERT: K 108 ASN cc_start: 0.7866 (m-40) cc_final: 0.7471 (p0) REVERT: L 121 MET cc_start: 0.8648 (mtp) cc_final: 0.8144 (mtp) REVERT: L 185 ASN cc_start: 0.7971 (t0) cc_final: 0.7484 (t0) REVERT: L 217 MET cc_start: 0.8132 (mtt) cc_final: 0.7742 (mtp) REVERT: N 25 MET cc_start: 0.8164 (mmm) cc_final: 0.7849 (tpt) REVERT: N 397 ILE cc_start: 0.9442 (mm) cc_final: 0.9171 (mt) REVERT: O 237 LYS cc_start: 0.9451 (mmtt) cc_final: 0.9049 (mmmm) REVERT: O 262 ASP cc_start: 0.8008 (p0) cc_final: 0.7193 (t0) REVERT: O 277 GLU cc_start: 0.8334 (tt0) cc_final: 0.7678 (tm-30) REVERT: O 321 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7828 (tm-30) REVERT: Q 374 MET cc_start: 0.7758 (mtp) cc_final: 0.7503 (mtp) REVERT: U 178 PHE cc_start: 0.7626 (m-80) cc_final: 0.7414 (m-10) REVERT: U 245 LYS cc_start: 0.8555 (mppt) cc_final: 0.8253 (mttt) REVERT: U 308 LYS cc_start: 0.8954 (mttt) cc_final: 0.8467 (tptt) REVERT: U 312 ILE cc_start: 0.8777 (mt) cc_final: 0.8422 (tp) REVERT: Y 81 ILE cc_start: 0.7989 (tp) cc_final: 0.7766 (tp) REVERT: Y 155 GLN cc_start: 0.8441 (mt0) cc_final: 0.8098 (mt0) REVERT: a 160 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7461 (mtp180) REVERT: a 179 GLN cc_start: 0.7818 (mt0) cc_final: 0.7200 (mp10) REVERT: d 53 HIS cc_start: 0.7260 (m-70) cc_final: 0.6218 (m-70) REVERT: d 120 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7067 (ptt90) REVERT: e 163 LYS cc_start: 0.8041 (tttt) cc_final: 0.7784 (ttmt) REVERT: e 222 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7638 (mtp85) REVERT: e 223 ARG cc_start: 0.7761 (tmt-80) cc_final: 0.7293 (tpm170) REVERT: f 50 LEU cc_start: 0.8358 (tp) cc_final: 0.7805 (mp) REVERT: f 51 ILE cc_start: 0.9023 (mm) cc_final: 0.8797 (mm) REVERT: f 64 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8055 (mt-10) REVERT: f 89 TYR cc_start: 0.9058 (m-10) cc_final: 0.8510 (m-80) REVERT: f 99 TYR cc_start: 0.7772 (m-10) cc_final: 0.7548 (m-10) REVERT: g 34 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7705 (ptm-80) REVERT: g 90 ARG cc_start: 0.7992 (mmt-90) cc_final: 0.7551 (ttp-170) REVERT: i 44 ARG cc_start: 0.7269 (mtt-85) cc_final: 0.6844 (mtt-85) REVERT: i 58 GLU cc_start: 0.8530 (tt0) cc_final: 0.7914 (tm-30) REVERT: i 80 ILE cc_start: 0.8461 (mm) cc_final: 0.8259 (mm) REVERT: i 104 ILE cc_start: 0.8911 (mm) cc_final: 0.8484 (mt) outliers start: 2 outliers final: 0 residues processed: 520 average time/residue: 0.4242 time to fit residues: 339.0919 Evaluate side-chains 385 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 3.138 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 HIS I 363 GLN 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 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 253 ASN ** O 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 155 GLN Y 158 GLN Z 102 GLN ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 HIS d 67 ASN e 174 GLN h 60 GLN h 67 ASN i 116 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30037 Z= 0.327 Angle : 0.663 10.023 41692 Z= 0.357 Chirality : 0.040 0.204 4949 Planarity : 0.005 0.138 4371 Dihedral : 23.993 174.143 6049 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.14 % 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: -0.17 (0.16), residues: 3051 helix: 1.07 (0.12), residues: 1935 sheet: -1.71 (0.34), residues: 236 loop : -2.31 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 472 HIS 0.009 0.001 HIS O 238 PHE 0.025 0.002 PHE Q 325 TYR 0.021 0.002 TYR d 87 ARG 0.015 0.001 ARG g 38 *********************** 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 473 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 471 time to evaluate : 4.009 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: H 112 LYS cc_start: 0.8620 (mptt) cc_final: 0.8384 (mptt) REVERT: I 364 LEU cc_start: 0.9440 (tp) cc_final: 0.9229 (mm) REVERT: I 580 MET cc_start: 0.7653 (ptm) cc_final: 0.7299 (ptm) REVERT: I 612 LYS cc_start: 0.8687 (mttt) cc_final: 0.8046 (tptp) REVERT: K 22 LYS cc_start: 0.8402 (mttt) cc_final: 0.8162 (mmtm) REVERT: K 108 ASN cc_start: 0.7759 (m-40) cc_final: 0.7362 (p0) REVERT: L 121 MET cc_start: 0.8717 (mtp) cc_final: 0.8106 (mtp) REVERT: L 198 MET cc_start: 0.8468 (mtp) cc_final: 0.8222 (mtp) REVERT: N 25 MET cc_start: 0.8346 (mmm) cc_final: 0.8010 (tpt) REVERT: N 159 ILE cc_start: 0.9616 (mt) cc_final: 0.9279 (tt) REVERT: O 237 LYS cc_start: 0.9375 (mmtt) cc_final: 0.8991 (mmmm) REVERT: O 262 ASP cc_start: 0.8087 (p0) cc_final: 0.7333 (t0) REVERT: Q 239 SER cc_start: 0.9047 (m) cc_final: 0.8542 (t) REVERT: U 178 PHE cc_start: 0.7783 (m-80) cc_final: 0.7537 (m-10) REVERT: U 308 LYS cc_start: 0.8977 (mttt) cc_final: 0.8528 (tttt) REVERT: U 312 ILE cc_start: 0.8654 (mt) cc_final: 0.8351 (tp) REVERT: Y 15 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6889 (mm-30) REVERT: a 158 PHE cc_start: 0.7652 (m-80) cc_final: 0.7444 (m-80) REVERT: a 179 GLN cc_start: 0.8062 (mt0) cc_final: 0.7214 (mp10) REVERT: d 41 TYR cc_start: 0.8498 (m-10) cc_final: 0.8139 (m-10) REVERT: d 66 LEU cc_start: 0.9187 (mm) cc_final: 0.8960 (mm) REVERT: d 120 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6845 (tmm160) REVERT: e 163 LYS cc_start: 0.8039 (tttt) cc_final: 0.7558 (mptt) REVERT: e 184 MET cc_start: 0.8362 (mmp) cc_final: 0.8005 (tmm) REVERT: e 223 ARG cc_start: 0.7839 (tmt-80) cc_final: 0.7490 (ttt180) REVERT: f 89 TYR cc_start: 0.9099 (m-10) cc_final: 0.8518 (m-80) REVERT: g 90 ARG cc_start: 0.7969 (mmt-90) cc_final: 0.7605 (ptt-90) REVERT: h 75 GLU cc_start: 0.8819 (tp30) cc_final: 0.8328 (tp30) REVERT: i 44 ARG cc_start: 0.7343 (mtt-85) cc_final: 0.7002 (mtt-85) REVERT: i 58 GLU cc_start: 0.8574 (tt0) cc_final: 0.7922 (tm-30) REVERT: i 104 ILE cc_start: 0.8881 (mm) cc_final: 0.8607 (mt) outliers start: 2 outliers final: 1 residues processed: 473 average time/residue: 0.4255 time to fit residues: 310.8474 Evaluate side-chains 354 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 3.096 ------------------------------------------------------------------------------- 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: 7.9990 chunk 227 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 320 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN K 107 GLN K 111 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 ASN ** 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** ** 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 h 67 ASN h 71 ASN i 114 HIS i 116 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30037 Z= 0.192 Angle : 0.575 13.241 41692 Z= 0.311 Chirality : 0.038 0.221 4949 Planarity : 0.004 0.160 4371 Dihedral : 23.925 173.249 6049 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % 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: 0.42 (0.16), residues: 3051 helix: 1.53 (0.12), residues: 1943 sheet: -1.35 (0.35), residues: 234 loop : -2.18 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 102 HIS 0.014 0.001 HIS a 200 PHE 0.037 0.001 PHE I 546 TYR 0.024 0.001 TYR d 87 ARG 0.008 0.000 ARG K 119 *********************** 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 478 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 477 time to evaluate : 3.127 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: I 580 MET cc_start: 0.7715 (ptm) cc_final: 0.7498 (ptm) REVERT: I 612 LYS cc_start: 0.8683 (mttt) cc_final: 0.8054 (tptp) REVERT: K 22 LYS cc_start: 0.8447 (mttt) cc_final: 0.8093 (mmtm) REVERT: K 96 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8106 (tm-30) REVERT: K 108 ASN cc_start: 0.7807 (m-40) cc_final: 0.7311 (p0) REVERT: L 121 MET cc_start: 0.8584 (mtp) cc_final: 0.8080 (mtp) REVERT: L 154 GLN cc_start: 0.8050 (mt0) cc_final: 0.7783 (tt0) REVERT: N 25 MET cc_start: 0.8284 (mmm) cc_final: 0.8053 (tpt) REVERT: N 159 ILE cc_start: 0.9587 (mt) cc_final: 0.9345 (tt) REVERT: N 217 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8226 (tmtt) REVERT: N 408 ASP cc_start: 0.8385 (t0) cc_final: 0.8056 (t70) REVERT: O 237 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8837 (mmmm) REVERT: O 262 ASP cc_start: 0.7787 (p0) cc_final: 0.7448 (t0) REVERT: O 305 MET cc_start: 0.7917 (tpp) cc_final: 0.7703 (tpp) REVERT: O 321 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7356 (tm-30) REVERT: P 143 ASP cc_start: 0.7983 (p0) cc_final: 0.7596 (p0) REVERT: P 325 LEU cc_start: 0.8622 (mt) cc_final: 0.8414 (mt) REVERT: Q 239 SER cc_start: 0.9208 (m) cc_final: 0.8733 (t) REVERT: U 178 PHE cc_start: 0.7785 (m-80) cc_final: 0.7544 (m-10) REVERT: U 299 MET cc_start: 0.9015 (mmp) cc_final: 0.8698 (mmp) REVERT: U 308 LYS cc_start: 0.8880 (mttt) cc_final: 0.8482 (tttt) REVERT: Y 15 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6812 (mm-30) REVERT: Y 155 GLN cc_start: 0.8359 (mt0) cc_final: 0.7953 (mp10) REVERT: a 179 GLN cc_start: 0.7949 (mt0) cc_final: 0.7332 (mp10) REVERT: d 41 TYR cc_start: 0.8277 (m-10) cc_final: 0.8041 (m-80) REVERT: d 53 HIS cc_start: 0.7105 (m90) cc_final: 0.6838 (m-70) REVERT: d 66 LEU cc_start: 0.9169 (mm) cc_final: 0.8969 (mm) REVERT: d 83 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7551 (ttpt) REVERT: d 120 ARG cc_start: 0.7812 (mtt180) cc_final: 0.6935 (ttp80) REVERT: e 163 LYS cc_start: 0.7956 (tttt) cc_final: 0.7756 (ttmt) REVERT: e 193 TYR cc_start: 0.8342 (t80) cc_final: 0.8132 (t80) REVERT: e 222 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7671 (mtp85) REVERT: e 223 ARG cc_start: 0.7841 (tmt-80) cc_final: 0.7401 (ttp-170) REVERT: f 92 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9173 (tmtt) REVERT: g 90 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7524 (ptt-90) REVERT: h 50 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6697 (mmtt) REVERT: h 75 GLU cc_start: 0.8746 (tp30) cc_final: 0.8224 (tp30) REVERT: h 87 TYR cc_start: 0.8813 (m-10) cc_final: 0.8469 (m-80) REVERT: i 44 ARG cc_start: 0.7272 (mtt-85) cc_final: 0.6818 (mtp85) REVERT: i 58 GLU cc_start: 0.8510 (tt0) cc_final: 0.7908 (tm-30) REVERT: i 104 ILE cc_start: 0.8833 (mm) cc_final: 0.8481 (mt) outliers start: 1 outliers final: 0 residues processed: 478 average time/residue: 0.4078 time to fit residues: 304.4990 Evaluate side-chains 360 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** L 101 GLN ** 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 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** h 67 ASN i 114 HIS i 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30037 Z= 0.260 Angle : 0.604 10.375 41692 Z= 0.326 Chirality : 0.038 0.178 4949 Planarity : 0.004 0.138 4371 Dihedral : 23.904 173.464 6049 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: 0.59 (0.16), residues: 3051 helix: 1.68 (0.12), residues: 1934 sheet: -1.25 (0.36), residues: 229 loop : -2.10 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.012 0.001 HIS a 200 PHE 0.030 0.002 PHE I 546 TYR 0.023 0.002 TYR P 156 ARG 0.010 0.000 ARG b 79 *********************** 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 463 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 3.294 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: I 445 MET cc_start: 0.8580 (tmm) cc_final: 0.8321 (mmp) REVERT: I 612 LYS cc_start: 0.8684 (mttt) cc_final: 0.8037 (tptp) REVERT: K 22 LYS cc_start: 0.8409 (mttt) cc_final: 0.8111 (mmtm) REVERT: K 96 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7923 (tm-30) REVERT: K 108 ASN cc_start: 0.7847 (m-40) cc_final: 0.7302 (p0) REVERT: L 121 MET cc_start: 0.8605 (mtp) cc_final: 0.8060 (mtp) REVERT: L 154 GLN cc_start: 0.8099 (mt0) cc_final: 0.7847 (tt0) REVERT: N 124 GLN cc_start: 0.8471 (mp10) cc_final: 0.8259 (mp10) REVERT: N 159 ILE cc_start: 0.9573 (mt) cc_final: 0.9332 (tt) REVERT: N 326 LEU cc_start: 0.9116 (mp) cc_final: 0.8761 (tp) REVERT: O 237 LYS cc_start: 0.9253 (mmtt) cc_final: 0.8942 (mmmm) REVERT: O 262 ASP cc_start: 0.7901 (p0) cc_final: 0.7518 (t0) REVERT: O 277 GLU cc_start: 0.8367 (tt0) cc_final: 0.8086 (tt0) REVERT: O 321 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7482 (tm-30) REVERT: P 143 ASP cc_start: 0.7995 (p0) cc_final: 0.7620 (p0) REVERT: Q 239 SER cc_start: 0.9149 (m) cc_final: 0.8713 (t) REVERT: U 299 MET cc_start: 0.9112 (mmp) cc_final: 0.8813 (mmp) REVERT: U 308 LYS cc_start: 0.8887 (mttt) cc_final: 0.8503 (tttt) REVERT: Y 15 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6853 (mm-30) REVERT: Y 155 GLN cc_start: 0.8359 (mt0) cc_final: 0.7940 (mp10) REVERT: a 179 GLN cc_start: 0.8003 (mt0) cc_final: 0.7264 (mp10) REVERT: d 53 HIS cc_start: 0.7187 (m90) cc_final: 0.6914 (m90) REVERT: d 120 ARG cc_start: 0.7803 (mtt180) cc_final: 0.6982 (ttp80) REVERT: e 146 GLN cc_start: 0.6694 (mp10) cc_final: 0.6261 (mp10) REVERT: e 184 MET cc_start: 0.8380 (mmp) cc_final: 0.8178 (mmp) REVERT: e 222 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7729 (mtp-110) REVERT: e 223 ARG cc_start: 0.7799 (tmt-80) cc_final: 0.7434 (ttp80) REVERT: f 86 ASP cc_start: 0.6466 (m-30) cc_final: 0.6263 (m-30) REVERT: g 90 ARG cc_start: 0.7929 (mmt-90) cc_final: 0.7529 (ptt-90) REVERT: h 50 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6674 (mmtt) REVERT: h 75 GLU cc_start: 0.8794 (tp30) cc_final: 0.8214 (tp30) REVERT: h 87 TYR cc_start: 0.8859 (m-10) cc_final: 0.8539 (m-80) REVERT: i 44 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.6844 (mtp85) REVERT: i 58 GLU cc_start: 0.8521 (tt0) cc_final: 0.7922 (tm-30) REVERT: i 104 ILE cc_start: 0.8837 (mm) cc_final: 0.8561 (mt) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.4218 time to fit residues: 305.4026 Evaluate side-chains 358 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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: 0.9990 chunk 288 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** 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** U 253 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 HIS ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 113 HIS e 207 HIS h 67 ASN i 114 HIS i 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30037 Z= 0.220 Angle : 0.594 11.054 41692 Z= 0.319 Chirality : 0.038 0.169 4949 Planarity : 0.004 0.146 4371 Dihedral : 23.875 173.251 6049 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 0.69 (0.16), residues: 3051 helix: 1.74 (0.12), residues: 1933 sheet: -1.14 (0.36), residues: 229 loop : -2.04 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.009 0.001 HIS a 200 PHE 0.025 0.002 PHE I 546 TYR 0.022 0.001 TYR P 156 ARG 0.007 0.000 ARG i 73 *********************** 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 467 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 2.627 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: I 536 ILE cc_start: 0.8497 (mm) cc_final: 0.7840 (tt) REVERT: I 612 LYS cc_start: 0.8676 (mttt) cc_final: 0.8066 (tptp) REVERT: K 22 LYS cc_start: 0.8443 (mttt) cc_final: 0.8115 (mmtm) REVERT: K 96 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8296 (tm-30) REVERT: K 108 ASN cc_start: 0.7821 (m-40) cc_final: 0.7281 (p0) REVERT: K 120 LYS cc_start: 0.8678 (mttt) cc_final: 0.8283 (tmtt) REVERT: L 85 MET cc_start: 0.7969 (tpp) cc_final: 0.7752 (tpt) REVERT: L 121 MET cc_start: 0.8528 (mtp) cc_final: 0.8002 (mtp) REVERT: L 154 GLN cc_start: 0.8108 (mt0) cc_final: 0.7824 (tt0) REVERT: N 124 GLN cc_start: 0.8368 (mp10) cc_final: 0.8147 (mp10) REVERT: N 159 ILE cc_start: 0.9576 (mt) cc_final: 0.9353 (tt) REVERT: N 255 MET cc_start: 0.9180 (tpt) cc_final: 0.8957 (tpt) REVERT: N 326 LEU cc_start: 0.9072 (mp) cc_final: 0.8726 (tp) REVERT: O 237 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8835 (mmmm) REVERT: O 262 ASP cc_start: 0.8014 (p0) cc_final: 0.7505 (t0) REVERT: O 277 GLU cc_start: 0.8372 (tt0) cc_final: 0.8111 (tt0) REVERT: O 321 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7512 (tm-30) REVERT: P 143 ASP cc_start: 0.8014 (p0) cc_final: 0.7623 (p0) REVERT: Q 239 SER cc_start: 0.9151 (m) cc_final: 0.8700 (t) REVERT: U 308 LYS cc_start: 0.8820 (mttt) cc_final: 0.8440 (tttt) REVERT: Y 15 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6851 (mm-30) REVERT: Y 82 MET cc_start: 0.7273 (tpp) cc_final: 0.6794 (tmm) REVERT: Y 96 GLU cc_start: 0.7998 (tp30) cc_final: 0.7730 (tp30) REVERT: a 179 GLN cc_start: 0.8088 (mt0) cc_final: 0.7352 (mp10) REVERT: d 41 TYR cc_start: 0.8426 (m-80) cc_final: 0.8088 (m-80) REVERT: d 53 HIS cc_start: 0.7131 (m90) cc_final: 0.6742 (m90) REVERT: d 120 ARG cc_start: 0.8011 (mtt180) cc_final: 0.6950 (ttp80) REVERT: e 184 MET cc_start: 0.8383 (mmp) cc_final: 0.8078 (mmp) REVERT: e 222 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7515 (mtp85) REVERT: e 223 ARG cc_start: 0.7794 (tmt-80) cc_final: 0.7088 (tpm170) REVERT: f 86 ASP cc_start: 0.6438 (m-30) cc_final: 0.6220 (m-30) REVERT: f 92 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9184 (tmtt) REVERT: g 34 ARG cc_start: 0.7928 (ptm-80) cc_final: 0.7720 (ptm-80) REVERT: g 90 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.7530 (ptt-90) REVERT: h 50 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6648 (mmtt) REVERT: h 75 GLU cc_start: 0.8794 (tp30) cc_final: 0.8527 (tp30) REVERT: h 87 TYR cc_start: 0.8839 (m-10) cc_final: 0.8525 (m-80) REVERT: i 44 ARG cc_start: 0.7257 (mtt-85) cc_final: 0.7021 (mtt-85) REVERT: i 58 GLU cc_start: 0.8447 (tt0) cc_final: 0.8152 (tm-30) REVERT: i 104 ILE cc_start: 0.8856 (mm) cc_final: 0.8494 (mt) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.4247 time to fit residues: 308.6563 Evaluate side-chains 353 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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: 0.0970 chunk 183 optimal weight: 0.2980 chunk 234 optimal weight: 0.1980 chunk 181 optimal weight: 0.4980 chunk 270 optimal weight: 10.0000 chunk 179 optimal weight: 0.3980 chunk 319 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN ** 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 155 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN e 207 HIS i 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30037 Z= 0.147 Angle : 0.570 11.606 41692 Z= 0.302 Chirality : 0.037 0.172 4949 Planarity : 0.004 0.127 4371 Dihedral : 23.706 173.278 6049 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % 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: 1.05 (0.16), residues: 3051 helix: 1.99 (0.12), residues: 1937 sheet: -0.92 (0.37), residues: 226 loop : -1.89 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.009 0.001 HIS a 200 PHE 0.026 0.001 PHE I 546 TYR 0.027 0.001 TYR f 73 ARG 0.007 0.000 ARG K 119 *********************** 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 477 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 3.061 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: H 56 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8114 (ttm-80) REVERT: I 401 CYS cc_start: 0.7785 (m) cc_final: 0.7532 (m) REVERT: I 445 MET cc_start: 0.8703 (tmm) cc_final: 0.8451 (mmp) REVERT: I 612 LYS cc_start: 0.8666 (mttt) cc_final: 0.8057 (tptp) REVERT: K 22 LYS cc_start: 0.8397 (mttt) cc_final: 0.8055 (mmtm) REVERT: K 108 ASN cc_start: 0.7906 (m-40) cc_final: 0.7484 (p0) REVERT: K 120 LYS cc_start: 0.8628 (mttt) cc_final: 0.8263 (tmtt) REVERT: L 85 MET cc_start: 0.7802 (tpp) cc_final: 0.7558 (tpt) REVERT: L 154 GLN cc_start: 0.8020 (mt0) cc_final: 0.7782 (tt0) REVERT: L 203 LEU cc_start: 0.9308 (mt) cc_final: 0.9087 (mt) REVERT: N 107 LEU cc_start: 0.9075 (tt) cc_final: 0.8860 (tp) REVERT: N 201 TYR cc_start: 0.8039 (m-80) cc_final: 0.7743 (m-10) REVERT: N 326 LEU cc_start: 0.9108 (mp) cc_final: 0.8667 (tp) REVERT: N 408 ASP cc_start: 0.8339 (t0) cc_final: 0.8049 (t70) REVERT: O 237 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8895 (mmmm) REVERT: O 262 ASP cc_start: 0.7874 (p0) cc_final: 0.7253 (t0) REVERT: O 321 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7386 (tm-30) REVERT: P 143 ASP cc_start: 0.7923 (p0) cc_final: 0.7530 (p0) REVERT: P 237 PHE cc_start: 0.8111 (p90) cc_final: 0.7874 (p90) REVERT: P 336 ASP cc_start: 0.8297 (p0) cc_final: 0.8075 (p0) REVERT: Q 239 SER cc_start: 0.9056 (m) cc_final: 0.8731 (t) REVERT: U 299 MET cc_start: 0.9064 (mmp) cc_final: 0.8807 (mmp) REVERT: U 308 LYS cc_start: 0.8782 (mttt) cc_final: 0.8439 (tttt) REVERT: Y 15 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6827 (mm-30) REVERT: Y 82 MET cc_start: 0.7249 (tpp) cc_final: 0.6677 (tmm) REVERT: a 179 GLN cc_start: 0.7965 (mt0) cc_final: 0.7259 (mp10) REVERT: b 69 ASP cc_start: 0.8067 (t70) cc_final: 0.7238 (t0) REVERT: d 67 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8329 (t0) REVERT: d 120 ARG cc_start: 0.7965 (mtt180) cc_final: 0.6925 (ttp80) REVERT: e 164 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7775 (tm-30) REVERT: e 223 ARG cc_start: 0.7820 (tmt-80) cc_final: 0.7320 (ttp-170) REVERT: g 90 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7424 (ptt-90) REVERT: h 50 LYS cc_start: 0.7002 (mmtt) cc_final: 0.6564 (mmtt) REVERT: h 54 PRO cc_start: 0.7742 (Cg_exo) cc_final: 0.6984 (Cg_endo) REVERT: h 75 GLU cc_start: 0.8750 (tp30) cc_final: 0.8233 (tp30) REVERT: h 87 TYR cc_start: 0.8796 (m-10) cc_final: 0.8436 (m-80) REVERT: i 44 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.6963 (mtt-85) REVERT: i 58 GLU cc_start: 0.8424 (tt0) cc_final: 0.8131 (tm-30) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.4019 time to fit residues: 302.2824 Evaluate side-chains 357 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 3.157 ------------------------------------------------------------------------------- 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: 0.6980 chunk 127 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 96 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 203 optimal weight: 0.3980 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 217 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30037 Z= 0.202 Angle : 0.587 11.355 41692 Z= 0.315 Chirality : 0.038 0.231 4949 Planarity : 0.004 0.123 4371 Dihedral : 23.710 173.829 6049 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % 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: 1.07 (0.16), residues: 3051 helix: 2.00 (0.12), residues: 1941 sheet: -0.90 (0.37), residues: 229 loop : -1.88 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.008 0.001 HIS a 200 PHE 0.034 0.002 PHE e 169 TYR 0.026 0.001 TYR d 125 ARG 0.006 0.000 ARG g 38 *********************** 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 455 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 454 time to evaluate : 3.170 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: H 112 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8203 (mmtt) REVERT: I 401 CYS cc_start: 0.7780 (m) cc_final: 0.7558 (m) REVERT: I 445 MET cc_start: 0.8640 (tmm) cc_final: 0.8430 (mmp) REVERT: I 612 LYS cc_start: 0.8683 (mttt) cc_final: 0.8064 (tptp) REVERT: I 702 MET cc_start: 0.7141 (ttm) cc_final: 0.6889 (ttp) REVERT: K 22 LYS cc_start: 0.8453 (mttt) cc_final: 0.8094 (mmtm) REVERT: K 96 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8139 (tm-30) REVERT: K 108 ASN cc_start: 0.8081 (m-40) cc_final: 0.7564 (p0) REVERT: K 120 LYS cc_start: 0.8600 (mttt) cc_final: 0.8240 (tmtt) REVERT: L 203 LEU cc_start: 0.9245 (mt) cc_final: 0.9011 (mt) REVERT: N 326 LEU cc_start: 0.9133 (mp) cc_final: 0.8899 (mt) REVERT: N 408 ASP cc_start: 0.8404 (t0) cc_final: 0.8155 (t70) REVERT: O 237 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8809 (mmmm) REVERT: O 262 ASP cc_start: 0.8006 (p0) cc_final: 0.7502 (t0) REVERT: Q 239 SER cc_start: 0.9110 (m) cc_final: 0.8704 (t) REVERT: Q 374 MET cc_start: 0.7651 (mtp) cc_final: 0.7328 (mtp) REVERT: U 305 LEU cc_start: 0.7882 (pt) cc_final: 0.7639 (pt) REVERT: U 308 LYS cc_start: 0.8788 (mttt) cc_final: 0.8429 (tttt) REVERT: Y 15 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6929 (mm-30) REVERT: Y 82 MET cc_start: 0.7301 (tpp) cc_final: 0.6894 (tmm) REVERT: Y 96 GLU cc_start: 0.7839 (tp30) cc_final: 0.7546 (tp30) REVERT: a 179 GLN cc_start: 0.7967 (mt0) cc_final: 0.7117 (mp10) REVERT: d 46 TYR cc_start: 0.6924 (t80) cc_final: 0.6715 (t80) REVERT: d 120 ARG cc_start: 0.7999 (mtt180) cc_final: 0.6932 (ttp80) REVERT: d 125 TYR cc_start: 0.5380 (t80) cc_final: 0.4803 (t80) REVERT: e 222 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7540 (mtp85) REVERT: e 223 ARG cc_start: 0.7857 (tmt-80) cc_final: 0.7044 (tpm170) REVERT: g 90 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7178 (ttp80) REVERT: h 50 LYS cc_start: 0.7013 (mmtt) cc_final: 0.6634 (mmtt) REVERT: h 75 GLU cc_start: 0.8744 (tp30) cc_final: 0.8270 (tp30) REVERT: h 87 TYR cc_start: 0.8780 (m-10) cc_final: 0.8497 (m-80) REVERT: i 58 GLU cc_start: 0.8460 (tt0) cc_final: 0.8130 (tm-30) REVERT: i 104 ILE cc_start: 0.8770 (mm) cc_final: 0.8347 (mt) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.4111 time to fit residues: 292.4342 Evaluate side-chains 353 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.886 ------------------------------------------------------------------------------- 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: 9.9990 chunk 306 optimal weight: 0.9980 chunk 279 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 234 optimal weight: 0.0050 chunk 91 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 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** U 217 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS d 67 ASN e 207 HIS i 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30037 Z= 0.163 Angle : 0.585 19.090 41692 Z= 0.309 Chirality : 0.038 0.251 4949 Planarity : 0.004 0.179 4371 Dihedral : 23.679 173.510 6049 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 0.04 % Allowed : 0.62 % Favored : 99.34 % 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: 1.19 (0.16), residues: 3051 helix: 2.09 (0.12), residues: 1937 sheet: -0.59 (0.39), residues: 220 loop : -1.86 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 102 HIS 0.008 0.001 HIS a 200 PHE 0.028 0.001 PHE e 169 TYR 0.024 0.001 TYR g 59 ARG 0.009 0.000 ARG g 38 *********************** 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 457 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 3.191 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: H 56 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8025 (ttm-80) REVERT: H 61 ILE cc_start: 0.8124 (mm) cc_final: 0.7915 (mt) REVERT: H 112 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8137 (mmtt) REVERT: I 401 CYS cc_start: 0.7766 (m) cc_final: 0.7525 (m) REVERT: I 440 MET cc_start: 0.8547 (mmm) cc_final: 0.8192 (mmm) REVERT: I 445 MET cc_start: 0.8587 (tmm) cc_final: 0.8333 (mmt) REVERT: I 468 MET cc_start: 0.8572 (tpp) cc_final: 0.8313 (tpp) REVERT: I 612 LYS cc_start: 0.8668 (mttt) cc_final: 0.8031 (tptp) REVERT: I 642 ILE cc_start: 0.8646 (mm) cc_final: 0.8395 (tp) REVERT: K 22 LYS cc_start: 0.8468 (mttt) cc_final: 0.8065 (mmtm) REVERT: K 96 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8129 (tm-30) REVERT: K 108 ASN cc_start: 0.7998 (m-40) cc_final: 0.7495 (p0) REVERT: K 120 LYS cc_start: 0.8575 (mttt) cc_final: 0.8242 (tmtt) REVERT: N 326 LEU cc_start: 0.9108 (mp) cc_final: 0.8723 (tp) REVERT: N 408 ASP cc_start: 0.8324 (t0) cc_final: 0.8115 (t70) REVERT: O 262 ASP cc_start: 0.7952 (p0) cc_final: 0.7481 (t0) REVERT: P 246 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7898 (mm-30) REVERT: Q 239 SER cc_start: 0.9089 (m) cc_final: 0.8692 (t) REVERT: U 308 LYS cc_start: 0.8728 (mttt) cc_final: 0.8391 (tttt) REVERT: Y 15 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6958 (mm-30) REVERT: Y 82 MET cc_start: 0.7260 (tpp) cc_final: 0.6808 (tmm) REVERT: Y 96 GLU cc_start: 0.7808 (tp30) cc_final: 0.7506 (tp30) REVERT: a 179 GLN cc_start: 0.7847 (mt0) cc_final: 0.7030 (mp10) REVERT: d 120 ARG cc_start: 0.7976 (mtt180) cc_final: 0.6910 (ttp80) REVERT: d 125 TYR cc_start: 0.5500 (t80) cc_final: 0.4952 (t80) REVERT: e 163 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7620 (mptt) REVERT: e 164 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7756 (tm-30) REVERT: e 223 ARG cc_start: 0.7834 (tmt-80) cc_final: 0.7047 (tpm170) REVERT: f 40 ARG cc_start: 0.8243 (mmp80) cc_final: 0.8021 (mmp80) REVERT: g 90 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7099 (ttp80) REVERT: h 50 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6592 (mmtt) REVERT: h 54 PRO cc_start: 0.7748 (Cg_exo) cc_final: 0.6982 (Cg_endo) REVERT: h 63 MET cc_start: 0.6715 (tmm) cc_final: 0.6273 (mmm) REVERT: h 75 GLU cc_start: 0.8715 (tp30) cc_final: 0.8247 (tp30) REVERT: h 87 TYR cc_start: 0.8749 (m-10) cc_final: 0.8495 (m-80) REVERT: i 44 ARG cc_start: 0.6539 (mtt-85) cc_final: 0.5616 (mmt-90) REVERT: i 58 GLU cc_start: 0.8461 (tt0) cc_final: 0.8128 (tm-30) outliers start: 1 outliers final: 1 residues processed: 457 average time/residue: 0.4104 time to fit residues: 291.0887 Evaluate side-chains 357 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 2.956 ------------------------------------------------------------------------------- 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: 3.9990 chunk 315 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 304 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 161 optimal weight: 0.0070 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 HIS ** N 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 217 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 HIS ** a 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 HIS b 76 HIS ** e 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3667 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= 0.264 Angle : 0.635 10.706 41692 Z= 0.339 Chirality : 0.039 0.188 4949 Planarity : 0.004 0.099 4371 Dihedral : 23.765 173.741 6049 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 1.03 (0.16), residues: 3051 helix: 1.97 (0.12), residues: 1938 sheet: -0.87 (0.38), residues: 225 loop : -1.91 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 89 HIS 0.009 0.001 HIS a 207 PHE 0.017 0.002 PHE I 512 TYR 0.029 0.002 TYR P 156 ARG 0.008 0.000 ARG Y 147 ********************** 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 430 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 GLN cc_start: 0.7977 (mt0) cc_final: 0.7524 (mt0) REVERT: H 112 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8043 (mmtt) REVERT: I 445 MET cc_start: 0.8651 (tmm) cc_final: 0.8428 (mmp) REVERT: I 468 MET cc_start: 0.8613 (tpp) cc_final: 0.8376 (tpp) REVERT: I 612 LYS cc_start: 0.8684 (mttt) cc_final: 0.8065 (tptp) REVERT: I 642 ILE cc_start: 0.8641 (mm) cc_final: 0.8396 (tp) REVERT: I 702 MET cc_start: 0.7096 (ttm) cc_final: 0.6855 (ttp) REVERT: K 22 LYS cc_start: 0.8497 (mttt) cc_final: 0.8101 (mmtm) REVERT: K 96 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8290 (tm-30) REVERT: K 108 ASN cc_start: 0.7994 (m-40) cc_final: 0.7542 (p0) REVERT: K 120 LYS cc_start: 0.8586 (mttt) cc_final: 0.8229 (tmtt) REVERT: L 198 MET cc_start: 0.8476 (mtp) cc_final: 0.8257 (mtp) REVERT: L 203 LEU cc_start: 0.9227 (mt) cc_final: 0.9018 (mt) REVERT: N 124 GLN cc_start: 0.8133 (mp10) cc_final: 0.7917 (mp10) REVERT: N 159 ILE cc_start: 0.9544 (mt) cc_final: 0.9343 (tt) REVERT: N 326 LEU cc_start: 0.9146 (mp) cc_final: 0.8926 (mt) REVERT: O 262 ASP cc_start: 0.8072 (p0) cc_final: 0.7509 (t0) REVERT: Q 239 SER cc_start: 0.9176 (m) cc_final: 0.8705 (t) REVERT: Q 374 MET cc_start: 0.7784 (mtp) cc_final: 0.7350 (mtp) REVERT: U 299 MET cc_start: 0.9016 (mmp) cc_final: 0.8678 (mmp) REVERT: U 305 LEU cc_start: 0.7855 (pt) cc_final: 0.7650 (pt) REVERT: U 308 LYS cc_start: 0.8752 (mttt) cc_final: 0.8398 (tttt) REVERT: Y 15 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6937 (mm-30) REVERT: Y 82 MET cc_start: 0.7268 (tpp) cc_final: 0.6733 (tmm) REVERT: a 179 GLN cc_start: 0.7954 (mt0) cc_final: 0.7321 (mp10) REVERT: a 183 ILE cc_start: 0.7608 (tp) cc_final: 0.7059 (mm) REVERT: b 60 LYS cc_start: 0.8518 (pptt) cc_final: 0.8299 (pptt) REVERT: d 120 ARG cc_start: 0.7996 (mtt180) cc_final: 0.6905 (ttp80) REVERT: d 125 TYR cc_start: 0.5561 (t80) cc_final: 0.4960 (t80) REVERT: e 146 GLN cc_start: 0.6213 (mp10) cc_final: 0.5953 (mp10) REVERT: e 223 ARG cc_start: 0.7835 (tmt-80) cc_final: 0.7048 (tpm170) REVERT: f 89 TYR cc_start: 0.9136 (m-10) cc_final: 0.8574 (m-80) REVERT: g 90 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.7295 (ptt-90) REVERT: h 50 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6737 (mmtt) REVERT: h 75 GLU cc_start: 0.8764 (tp30) cc_final: 0.8544 (tp30) REVERT: i 58 GLU cc_start: 0.8500 (tt0) cc_final: 0.8141 (tm-30) REVERT: i 104 ILE cc_start: 0.8739 (mm) cc_final: 0.8295 (mt) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.4162 time to fit residues: 285.0664 Evaluate side-chains 344 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.384 ------------------------------------------------------------------------------- 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: 9.9990 chunk 280 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 270 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 HIS ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 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 ** Y 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Z 103 GLN a 207 HIS b 76 HIS d 67 ASN ** e 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.108641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086961 restraints weight = 108411.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088448 restraints weight = 226117.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089316 restraints weight = 107564.863| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30037 Z= 0.254 Angle : 0.626 10.957 41692 Z= 0.336 Chirality : 0.039 0.173 4949 Planarity : 0.004 0.097 4371 Dihedral : 23.836 173.184 6049 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % 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: 1.00 (0.16), residues: 3051 helix: 1.95 (0.12), residues: 1938 sheet: -0.90 (0.38), residues: 222 loop : -1.91 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.013 0.001 HIS a 207 PHE 0.020 0.002 PHE Z 65 TYR 0.033 0.002 TYR P 156 ARG 0.010 0.000 ARG g 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6083.70 seconds wall clock time: 110 minutes 49.49 seconds (6649.49 seconds total)