Starting phenix.real_space_refine on Sat Feb 24 06:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zi4_14737/02_2024/7zi4_14737_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zi4_14737/02_2024/7zi4_14737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zi4_14737/02_2024/7zi4_14737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zi4_14737/02_2024/7zi4_14737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zi4_14737/02_2024/7zi4_14737_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zi4_14737/02_2024/7zi4_14737_updated.pdb" } resolution = 3.2 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= 0.003 sd= 1.133 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 331 5.49 5 S 158 5.16 5 Be 1 3.05 5 C 25618 2.51 5 N 7565 2.21 5 O 8617 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "R GLU 4": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42294 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3323 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3261 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3394 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3356 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 427} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3402 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3335 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 4962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 4962 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 816 Unresolved non-hydrogen dihedrals: 530 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 378 Chain: "N" 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: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 758 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3109 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "Q" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 735 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "I" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 751 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 747 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 839 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3223 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "Y" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3252 Classifications: {'DNA': 158} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 157} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26163 SG CYS R 309 13.916 62.361 140.805 1.00142.09 S ATOM 26193 SG CYS R 314 13.612 63.046 144.568 1.00143.88 S ATOM 26312 SG CYS R 330 17.008 62.330 143.328 1.00133.28 S ATOM 26341 SG CYS R 334 14.621 59.563 143.201 1.00136.57 S Time building chain proxies: 21.09, per 1000 atoms: 0.50 Number of scatterers: 42294 At special positions: 0 Unit cell: (134.2, 189.2, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 158 16.00 P 331 15.00 F 3 9.00 O 8617 8.00 N 7565 7.00 C 25618 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.77 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 334 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 330 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 314 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 309 " Number of angles added : 6 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 32 sheets defined 42.7% alpha, 11.0% beta 146 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 18.74 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.751A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.619A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.663A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.817A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 388 through 400 Processing helix chain 'A' and resid 404 through 419 removed outlier: 4.300A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.633A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.613A pdb=" N ASP A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.702A pdb=" N ARG B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.831A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.620A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.907A pdb=" N SER B 262 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 286 removed outlier: 3.549A pdb=" N GLU B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.575A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.986A pdb=" N ARG B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 378 Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.935A pdb=" N THR B 388 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 415 removed outlier: 3.664A pdb=" N ILE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.600A pdb=" N ARG B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 removed outlier: 4.282A pdb=" N GLU B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR B 446 " --> pdb=" O TYR B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.712A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.782A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.694A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.273A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.610A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 403 through 419 removed outlier: 3.613A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.943A pdb=" N SER D 262 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 286 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.593A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.959A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.563A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 399 through 415 removed outlier: 3.681A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 436 through 446 removed outlier: 4.328A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 Processing helix chain 'E' and resid 76 through 87 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 174 through 180 Processing helix chain 'E' and resid 240 through 248 removed outlier: 3.550A pdb=" N ASP E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 273 through 288 removed outlier: 3.600A pdb=" N LYS E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 309 through 319 removed outlier: 3.875A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 352 through 357 removed outlier: 4.285A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 382 Processing helix chain 'E' and resid 388 through 401 removed outlier: 3.788A pdb=" N HIS E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 420 removed outlier: 3.811A pdb=" N LEU E 409 " --> pdb=" O TYR E 405 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Proline residue: E 412 - end of helix Processing helix chain 'E' and resid 427 through 436 Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 451 through 453 No H-bonds generated for 'chain 'E' and resid 451 through 453' Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 105 through 108 removed outlier: 4.228A pdb=" N ILE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.734A pdb=" N ALA F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 185 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 257 through 262 removed outlier: 4.207A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 286 removed outlier: 3.684A pdb=" N GLU F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.695A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 4.917A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 377 removed outlier: 3.897A pdb=" N ILE F 373 " --> pdb=" O GLN F 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.793A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 436 through 445 removed outlier: 3.582A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 535 Processing helix chain 'G' and resid 549 through 559 Processing helix chain 'G' and resid 577 through 589 removed outlier: 4.085A pdb=" N ASN G 580 " --> pdb=" O SER G 577 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN G 581 " --> pdb=" O THR G 578 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP G 582 " --> pdb=" O LEU G 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 588 " --> pdb=" O GLU G 585 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE G 589 " --> pdb=" O PHE G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 612 removed outlier: 3.778A pdb=" N TRP G 612 " --> pdb=" O ILE G 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 636 Processing helix chain 'G' and resid 638 through 642 Processing helix chain 'G' and resid 654 through 656 No H-bonds generated for 'chain 'G' and resid 654 through 656' Processing helix chain 'G' and resid 663 through 669 Processing helix chain 'G' and resid 688 through 698 Processing helix chain 'G' and resid 706 through 711 Processing helix chain 'G' and resid 730 through 740 Processing helix chain 'G' and resid 769 through 779 Processing helix chain 'G' and resid 810 through 817 Processing helix chain 'G' and resid 842 through 847 Processing helix chain 'G' and resid 850 through 853 No H-bonds generated for 'chain 'G' and resid 850 through 853' Processing helix chain 'G' and resid 855 through 863 removed outlier: 4.182A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) Processing helix chain 'G' and resid 869 through 877 Processing helix chain 'G' and resid 889 through 893 Processing helix chain 'G' and resid 898 through 906 removed outlier: 3.680A pdb=" N ALA G 902 " --> pdb=" O PRO G 898 " (cutoff:3.500A) Processing helix chain 'G' and resid 909 through 932 removed outlier: 4.921A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 959 through 964 Processing helix chain 'G' and resid 966 through 971 removed outlier: 3.805A pdb=" N SER G 970 " --> pdb=" O PRO G 966 " (cutoff:3.500A) Processing helix chain 'G' and resid 1008 through 1010 No H-bonds generated for 'chain 'G' and resid 1008 through 1010' Processing helix chain 'G' and resid 1029 through 1040 removed outlier: 3.629A pdb=" N GLU G1040 " --> pdb=" O ARG G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1044 through 1052 Processing helix chain 'G' and resid 1055 through 1066 removed outlier: 4.843A pdb=" N ARG G1065 " --> pdb=" O TRP G1061 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER G1066 " --> pdb=" O LEU G1062 " (cutoff:3.500A) Processing helix chain 'G' and resid 1093 through 1099 removed outlier: 3.684A pdb=" N ASP G1099 " --> pdb=" O LEU G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1101 through 1116 Processing helix chain 'G' and resid 1127 through 1139 Processing helix chain 'G' and resid 1153 through 1163 Processing helix chain 'G' and resid 1176 through 1179 No H-bonds generated for 'chain 'G' and resid 1176 through 1179' Processing helix chain 'G' and resid 1203 through 1210 Processing helix chain 'G' and resid 1231 through 1248 Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 31 through 41 Processing helix chain 'N' and resid 50 through 75 removed outlier: 3.700A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU N 63 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL N 65 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE N 66 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 93 removed outlier: 3.838A pdb=" N VAL N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 27 Processing helix chain 'R' and resid 332 through 341 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 144 through 156 removed outlier: 4.090A pdb=" N CYS H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 215 through 229 Processing helix chain 'H' and resid 239 through 248 Processing helix chain 'H' and resid 256 through 262 Processing helix chain 'H' and resid 266 through 269 No H-bonds generated for 'chain 'H' and resid 266 through 269' Processing helix chain 'H' and resid 447 through 450 No H-bonds generated for 'chain 'H' and resid 447 through 450' Processing helix chain 'H' and resid 452 through 454 No H-bonds generated for 'chain 'H' and resid 452 through 454' Processing helix chain 'H' and resid 458 through 460 No H-bonds generated for 'chain 'H' and resid 458 through 460' Processing helix chain 'H' and resid 468 through 476 removed outlier: 3.737A pdb=" N LEU H 472 " --> pdb=" O ILE H 468 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN H 473 " --> pdb=" O ALA H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 488 removed outlier: 3.753A pdb=" N GLU H 485 " --> pdb=" O LYS H 481 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET H 486 " --> pdb=" O ASP H 482 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 487 " --> pdb=" O ILE H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 514 removed outlier: 3.539A pdb=" N MET H 514 " --> pdb=" O GLU H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 532 through 542 Processing helix chain 'H' and resid 555 through 559 Processing helix chain 'Q' and resid 144 through 153 removed outlier: 3.853A pdb=" N ALA Q 153 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 200 through 208 Processing helix chain 'Q' and resid 211 through 220 Processing helix chain 'I' and resid 46 through 54 Processing helix chain 'I' and resid 64 through 78 removed outlier: 4.130A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 113 Processing helix chain 'I' and resid 121 through 131 removed outlier: 3.621A pdb=" N LEU I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 28 Processing helix chain 'J' and resid 31 through 41 Processing helix chain 'J' and resid 50 through 75 removed outlier: 3.897A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG J 67 " --> pdb=" O GLU J 63 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'K' and resid 17 through 21 Processing helix chain 'K' and resid 27 through 36 Processing helix chain 'K' and resid 45 through 72 removed outlier: 4.500A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'L' and resid 38 through 48 Processing helix chain 'L' and resid 56 through 83 removed outlier: 3.752A pdb=" N ARG L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS L 82 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 101 removed outlier: 3.925A pdb=" N THR L 96 " --> pdb=" O ARG L 92 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG L 99 " --> pdb=" O GLN L 95 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 122 Processing helix chain 'M' and resid 45 through 54 Processing helix chain 'M' and resid 64 through 78 Processing helix chain 'M' and resid 86 through 114 Processing helix chain 'M' and resid 121 through 131 Processing helix chain 'O' and resid 17 through 21 Processing helix chain 'O' and resid 27 through 36 Processing helix chain 'O' and resid 47 through 73 removed outlier: 3.601A pdb=" N ASP O 72 " --> pdb=" O ASN O 68 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 88 Processing helix chain 'O' and resid 91 through 96 Processing helix chain 'O' and resid 113 through 115 No H-bonds generated for 'chain 'O' and resid 113 through 115' Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.997A pdb=" N LYS P 43 " --> pdb=" O ILE P 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS P 46 " --> pdb=" O TYR P 42 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN P 47 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL P 48 " --> pdb=" O VAL P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 83 Processing helix chain 'P' and resid 91 through 101 Processing helix chain 'P' and resid 105 through 122 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.610A pdb=" N MET A 359 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 327 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU A 68 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A 329 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY A 70 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER A 331 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 292 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 130 through 134 removed outlier: 3.585A pdb=" N ALA A 199 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 138 through 140 removed outlier: 3.617A pdb=" N GLY A 166 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.903A pdb=" N ALA B 72 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL B 357 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 74 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 327 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 233 through 243 Processing sheet with id= G, first strand: chain 'B' and resid 169 through 174 removed outlier: 4.088A pdb=" N GLY B 159 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 144 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS B 164 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL B 142 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 191 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 206 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR B 194 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS B 204 " --> pdb=" O THR B 194 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP B 196 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 202 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 358 through 362 removed outlier: 7.201A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 327 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU C 68 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 329 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 229 through 239 removed outlier: 3.825A pdb=" N VAL C 295 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 167 through 172 removed outlier: 3.857A pdb=" N GLU C 137 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS C 162 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL C 135 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP C 189 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY C 204 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR C 192 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU C 194 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 200 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= L, first strand: chain 'D' and resid 354 through 358 removed outlier: 7.041A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 75 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 296 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 327 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 233 through 243 Processing sheet with id= N, first strand: chain 'D' and resid 169 through 174 removed outlier: 4.117A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 158 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 144 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS D 164 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL D 142 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP D 191 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 206 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR D 194 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS D 204 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP D 196 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 202 " --> pdb=" O ASP D 196 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 358 through 363 removed outlier: 6.963A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR E 363 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 69 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 327 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LEU E 68 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE E 329 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLY E 70 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER E 331 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 292 through 296 Processing sheet with id= Q, first strand: chain 'E' and resid 130 through 134 removed outlier: 3.910A pdb=" N GLY E 204 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR E 192 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLU E 194 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL E 200 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 157 through 162 Processing sheet with id= S, first strand: chain 'E' and resid 335 through 337 Processing sheet with id= T, first strand: chain 'F' and resid 356 through 358 removed outlier: 8.037A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 327 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 233 through 243 Processing sheet with id= V, first strand: chain 'F' and resid 138 through 141 removed outlier: 3.685A pdb=" N GLY F 206 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR F 194 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS F 204 " --> pdb=" O THR F 194 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASP F 196 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 202 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'F' and resid 332 through 334 Processing sheet with id= Y, first strand: chain 'G' and resid 626 through 629 removed outlier: 6.631A pdb=" N PHE G 570 " --> pdb=" O VAL G 627 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR G 629 " --> pdb=" O PHE G 570 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE G 572 " --> pdb=" O THR G 629 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR G 648 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE G 573 " --> pdb=" O TYR G 648 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 650 " --> pdb=" O ILE G 573 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 759 through 765 removed outlier: 3.569A pdb=" N PHE G1193 " --> pdb=" O TYR G1222 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 831 through 833 Processing sheet with id= AB, first strand: chain 'G' and resid 987 through 989 Processing sheet with id= AC, first strand: chain 'G' and resid 980 through 984 removed outlier: 6.896A pdb=" N THR G1004 " --> pdb=" O SER G 981 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR G 983 " --> pdb=" O LEU G1002 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU G1002 " --> pdb=" O TYR G 983 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 274 through 277 removed outlier: 3.674A pdb=" N ARG R 274 " --> pdb=" O SER R 285 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.505A pdb=" N GLY H 45 " --> pdb=" O VAL H 34 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 523 through 525 removed outlier: 6.475A pdb=" N VAL H 491 " --> pdb=" O GLN H 524 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU H 184 " --> pdb=" O PHE H 492 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR H 494 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE H 186 " --> pdb=" O THR H 494 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS H 209 " --> pdb=" O VAL H 195 " (cutoff:3.500A) 1393 hydrogen bonds defined for protein. 4056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 20.96 Time building geometry restraints manager: 18.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10722 1.33 - 1.45: 9220 1.45 - 1.57: 22795 1.57 - 1.69: 655 1.69 - 1.81: 262 Bond restraints: 43654 Sorted by residual: bond pdb=" BE BEF G1602 " pdb=" F2 BEF G1602 " ideal model delta sigma weight residual 1.476 1.708 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" BE BEF G1602 " pdb=" F1 BEF G1602 " ideal model delta sigma weight residual 1.476 1.703 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" BE BEF G1602 " pdb=" F3 BEF G1602 " ideal model delta sigma weight residual 1.476 1.688 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" N MET E 147 " pdb=" CA MET E 147 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.20e+00 bond pdb=" CA SER P 36 " pdb=" CB SER P 36 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.69e-02 3.50e+03 6.24e+00 ... (remaining 43649 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.59: 2153 105.59 - 113.24: 24513 113.24 - 120.89: 20571 120.89 - 128.54: 12797 128.54 - 136.19: 415 Bond angle restraints: 60449 Sorted by residual: angle pdb=" F1 BEF G1602 " pdb=" BE BEF G1602 " pdb=" F3 BEF G1602 " ideal model delta sigma weight residual 120.12 98.84 21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" C3' DC X -70 " pdb=" O3' DC X -70 " pdb=" P DT X -69 " ideal model delta sigma weight residual 120.20 112.03 8.17 1.50e+00 4.44e-01 2.96e+01 angle pdb=" F2 BEF G1602 " pdb=" BE BEF G1602 " pdb=" F3 BEF G1602 " ideal model delta sigma weight residual 119.96 105.16 14.80 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N TYR P 37 " pdb=" CA TYR P 37 " pdb=" C TYR P 37 " ideal model delta sigma weight residual 112.88 106.69 6.19 1.29e+00 6.01e-01 2.30e+01 angle pdb=" C PHE G 822 " pdb=" N GLU G 823 " pdb=" CA GLU G 823 " ideal model delta sigma weight residual 122.92 115.04 7.88 1.75e+00 3.27e-01 2.03e+01 ... (remaining 60444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 23969 35.42 - 70.84: 1620 70.84 - 106.27: 45 106.27 - 141.69: 4 141.69 - 177.11: 6 Dihedral angle restraints: 25644 sinusoidal: 12144 harmonic: 13500 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 128.73 171.27 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 130.02 169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 130.27 169.73 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 25641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 6707 0.100 - 0.200: 247 0.200 - 0.299: 1 0.299 - 0.399: 0 0.399 - 0.499: 3 Chirality restraints: 6958 Sorted by residual: chirality pdb=" P DC X -70 " pdb=" OP1 DC X -70 " pdb=" OP2 DC X -70 " pdb=" O5' DC X -70 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" P DT X -69 " pdb=" OP1 DT X -69 " pdb=" OP2 DT X -69 " pdb=" O5' DT X -69 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" P DC X -68 " pdb=" OP1 DC X -68 " pdb=" OP2 DC X -68 " pdb=" O5' DC X -68 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 6955 not shown) Planarity restraints: 6640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 590 " -0.087 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO G 591 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO G 591 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO G 591 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 575 " -0.070 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO H 576 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO H 576 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO H 576 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 109 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR E 109 " -0.071 2.00e-02 2.50e+03 pdb=" O THR E 109 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU E 110 " 0.024 2.00e-02 2.50e+03 ... (remaining 6637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 683 2.66 - 3.22: 38669 3.22 - 3.78: 67779 3.78 - 4.34: 90362 4.34 - 4.90: 140833 Nonbonded interactions: 338326 Sorted by model distance: nonbonded pdb=" O2 DC X -30 " pdb=" N2 DG Y 30 " model vdw 2.100 2.496 nonbonded pdb=" O3B ADP G1601 " pdb=" BE BEF G1602 " model vdw 2.115 2.420 nonbonded pdb=" OH TYR B 401 " pdb=" O PHE B 433 " model vdw 2.158 2.440 nonbonded pdb=" OG1 THR P 90 " pdb=" OE1 GLU P 93 " model vdw 2.166 2.440 nonbonded pdb=" O2 DC X -43 " pdb=" N2 DG Y 43 " model vdw 2.167 2.496 ... (remaining 338321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 141 or (resid 152 through 153 and \ (name N or name CA or name C or name O or name CB )) or resid 154 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 through 184 or (resid 185 and (name N or name CA or name C or name O or name C \ B )) or resid 186 through 284 or (resid 285 and (name N or name CA or name C or \ name O or name CB )) or resid 286 through 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB )) or resid 347 through 438 or (resid 439 thro \ ugh 440 and (name N or name CA or name C or name O or name CB )) or resid 441 or \ (resid 442 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 3 through 452 or (resid 453 and (name N or name CA or name C or name O or name C \ B )) or resid 454 or resid 501)) selection = (chain 'C' and (resid 12 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 141 or resid 152 through 184 or (r \ esid 185 and (name N or name CA or name C or name O or name CB )) or resid 186 t \ hrough 231 or (resid 232 and (name N or name CA or name C or name O or name CB ) \ ) or resid 233 through 253 or (resid 254 through 257 and (name N or name CA or n \ ame C or name O or name CB )) or resid 258 through 302 or (resid 303 and (name N \ or name CA or name C or name O or name CB )) or resid 304 through 441 or (resid \ 442 and (name N or name CA or name C or name O or name CB )) or resid 443 throu \ gh 454 or resid 501)) selection = (chain 'E' and (resid 12 through 141 or (resid 152 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )) or resid 158 through 231 \ or (resid 232 and (name N or name CA or name C or name O or name CB )) or resid \ 233 through 253 or (resid 254 through 257 and (name N or name CA or name C or n \ ame O or name CB )) or resid 258 through 284 or (resid 285 and (name N or name C \ A or name C or name O or name CB )) or resid 286 through 302 or (resid 303 and ( \ name N or name CA or name C or name O or name CB )) or resid 304 through 345 or \ (resid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 \ through 438 or (resid 439 through 440 and (name N or name CA or name C or name \ O or name CB )) or resid 441 through 452 or (resid 453 and (name N or name CA or \ name C or name O or name CB )) or resid 454 or resid 501)) } ncs_group { reference = (chain 'B' and (resid 15 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161 through 168 or (resid 169 \ and (name N or name CA or name C or name O or name CB )) or resid 170 through 20 \ 8 or (resid 209 and (name N or name CA or name C or name O or name CB )) or resi \ d 210 through 245 or (resid 246 and (name N or name CA or name C or name O or na \ me CB )) or resid 247 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 363 or (resid 364 and (name N or n \ ame CA or name C or name O or name CB )) or resid 365 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 44 \ 3 or (resid 444 through 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 through 453 or resid 501)) selection = (chain 'D' and (resid 15 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 or (resid 63 and (name N or n \ ame CA or name C or name O or name CB )) or resid 64 through 66 or (resid 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 148 or \ (resid 149 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 56 through 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 159 or (resid 160 and (name N or name CA or name C or name O or nam \ e CB )) or resid 161 through 168 or (resid 169 and (name N or name CA or name C \ or name O or name CB )) or resid 170 through 214 or resid 222 through 245 or (re \ sid 246 and (name N or name CA or name C or name O or name CB )) or resid 247 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 391 or (resid 392 and (name N or name CA or name C or name \ O or name CB )) or resid 393 through 395 or (resid 396 and (name N or name CA o \ r name C or name O or name CB )) or resid 397 through 443 or (resid 444 through \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 throug \ h 453 or resid 501)) selection = (chain 'F' and (resid 15 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 66 or (resid 67 and ( \ name N or name CA or name C or name O or name CB )) or resid 68 through 149 or r \ esid 156 through 208 or (resid 209 and (name N or name CA or name C or name O or \ name CB )) or resid 210 or (resid 211 through 214 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 222 through 223 and (name N or name CA or \ name C or name O or name CB )) or resid 224 through 278 or (resid 279 and (name \ N or name CA or name C or name O or name CB )) or resid 280 through 348 or (resi \ d 349 and (name N or name CA or name C or name O or name CB )) or resid 350 thro \ ugh 363 or (resid 364 and (name N or name CA or name C or name O or name CB )) o \ r resid 365 through 391 or (resid 392 and (name N or name CA or name C or name O \ or name CB )) or resid 393 through 395 or (resid 396 and (name N or name CA or \ name C or name O or name CB )) or resid 397 through 426 or (resid 427 and (name \ N or name CA or name C or name O or name CB )) or resid 428 through 453 or resid \ 501)) } ncs_group { reference = (chain 'I' and (resid 43 through 133 or (resid 134 through 135 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 43 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 135)) } ncs_group { reference = (chain 'J' and resid 24 through 102) selection = (chain 'N' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O )))) } ncs_group { reference = (chain 'K' and ((resid 13 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 117 or (resid 118 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'O' and resid 13 through 118) } ncs_group { reference = (chain 'L' and (resid 31 through 115 or (resid 116 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 123)) selection = (chain 'P' and (resid 31 through 119 or (resid 120 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.500 Check model and map are aligned: 0.610 Set scattering table: 0.400 Process input model: 128.780 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.003 0.232 43654 Z= 0.190 Angle : 0.612 21.282 60449 Z= 0.321 Chirality : 0.041 0.499 6958 Planarity : 0.005 0.135 6640 Dihedral : 19.742 177.109 16936 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.95 % Favored : 94.83 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.45 % 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: -0.70 (0.12), residues: 4626 helix: 0.31 (0.12), residues: 2155 sheet: -0.33 (0.20), residues: 643 loop : -1.37 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 712 HIS 0.005 0.001 HIS R 27 PHE 0.031 0.001 PHE G 853 TYR 0.029 0.001 TYR G1144 ARG 0.013 0.000 ARG Q 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 448 time to evaluate : 4.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.6656 (mmt) cc_final: 0.6388 (mmt) REVERT: C 278 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 274 GLU cc_start: 0.7646 (mp0) cc_final: 0.7443 (mp0) REVERT: F 213 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7988 (tpp80) REVERT: G 559 HIS cc_start: 0.6199 (m170) cc_final: 0.5965 (t70) REVERT: R 327 GLN cc_start: 0.7266 (mp10) cc_final: 0.6836 (mp10) REVERT: H 46 TRP cc_start: 0.7399 (m100) cc_final: 0.7154 (m-10) REVERT: H 242 MET cc_start: 0.8224 (mmp) cc_final: 0.8019 (mmp) REVERT: H 504 LYS cc_start: 0.7227 (tttt) cc_final: 0.6914 (ttpp) REVERT: H 555 LYS cc_start: 0.9194 (tmmt) cc_final: 0.8980 (tptt) REVERT: Q 206 ILE cc_start: 0.8979 (tt) cc_final: 0.8745 (pt) REVERT: I 80 THR cc_start: 0.8460 (p) cc_final: 0.8122 (p) REVERT: J 27 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8079 (mm-40) REVERT: L 37 TYR cc_start: 0.8498 (m-80) cc_final: 0.8286 (m-80) outliers start: 8 outliers final: 3 residues processed: 455 average time/residue: 0.5158 time to fit residues: 395.8379 Evaluate side-chains 364 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 361 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain P residue 36 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 384 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 444 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 43654 Z= 0.330 Angle : 0.628 8.777 60449 Z= 0.328 Chirality : 0.042 0.218 6958 Planarity : 0.004 0.080 6640 Dihedral : 21.705 168.981 8622 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 1.40 % Allowed : 8.52 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4626 helix: 0.44 (0.11), residues: 2180 sheet: -0.44 (0.19), residues: 671 loop : -1.46 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 712 HIS 0.006 0.001 HIS N 75 PHE 0.027 0.002 PHE G 853 TYR 0.024 0.002 TYR G1136 ARG 0.009 0.001 ARG Q 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 361 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 308 ASP cc_start: 0.8151 (t0) cc_final: 0.7794 (t0) REVERT: D 274 GLU cc_start: 0.7852 (mp0) cc_final: 0.7637 (mp0) REVERT: F 213 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7983 (tpp80) REVERT: F 326 MET cc_start: 0.8250 (mtt) cc_final: 0.7921 (mtt) REVERT: F 443 MET cc_start: 0.6599 (ttt) cc_final: 0.6392 (ttt) REVERT: G 559 HIS cc_start: 0.6466 (m170) cc_final: 0.6209 (t70) REVERT: G 775 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: N 92 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7117 (ttp80) REVERT: R 11 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6071 (tm-30) REVERT: R 327 GLN cc_start: 0.7287 (mp10) cc_final: 0.6835 (mp10) REVERT: H 46 TRP cc_start: 0.7505 (m100) cc_final: 0.7199 (m100) REVERT: H 504 LYS cc_start: 0.7409 (tttt) cc_final: 0.7020 (ttpp) REVERT: H 555 LYS cc_start: 0.9319 (tmmt) cc_final: 0.9094 (tptt) REVERT: Q 206 ILE cc_start: 0.9009 (tt) cc_final: 0.8734 (pt) REVERT: J 24 ASP cc_start: 0.6794 (t70) cc_final: 0.6537 (t0) REVERT: O 56 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7610 (mm-30) outliers start: 51 outliers final: 38 residues processed: 389 average time/residue: 0.5025 time to fit residues: 332.7828 Evaluate side-chains 372 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 333 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 1138 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain Q residue 181 VAL Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 370 optimal weight: 0.9990 chunk 303 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 445 optimal weight: 0.7980 chunk 481 optimal weight: 5.9990 chunk 397 optimal weight: 0.8980 chunk 442 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 357 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1142 HIS ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43654 Z= 0.171 Angle : 0.537 9.855 60449 Z= 0.281 Chirality : 0.039 0.207 6958 Planarity : 0.003 0.050 6640 Dihedral : 21.491 178.315 8622 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 1.43 % Allowed : 11.46 % Favored : 87.11 % 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: -0.21 (0.12), residues: 4626 helix: 0.87 (0.12), residues: 2172 sheet: -0.34 (0.20), residues: 663 loop : -1.27 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP G 712 HIS 0.004 0.001 HIS K 82 PHE 0.021 0.001 PHE G 853 TYR 0.015 0.001 TYR J 51 ARG 0.006 0.000 ARG M 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 371 time to evaluate : 4.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8057 (t) REVERT: B 161 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8254 (pt) REVERT: C 216 GLU cc_start: 0.7680 (tp30) cc_final: 0.6400 (pt0) REVERT: D 144 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: D 282 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: D 326 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: F 213 ARG cc_start: 0.8273 (tpp80) cc_final: 0.8016 (tpp80) REVERT: F 326 MET cc_start: 0.8270 (mtt) cc_final: 0.7951 (mtt) REVERT: G 775 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: N 58 LEU cc_start: 0.8689 (tp) cc_final: 0.8390 (tp) REVERT: R 327 GLN cc_start: 0.7187 (mp10) cc_final: 0.6842 (mp10) REVERT: H 46 TRP cc_start: 0.7547 (m100) cc_final: 0.7223 (m100) REVERT: H 504 LYS cc_start: 0.7252 (tttt) cc_final: 0.6975 (ttpp) REVERT: H 555 LYS cc_start: 0.9313 (tmmt) cc_final: 0.9102 (tptt) REVERT: Q 206 ILE cc_start: 0.8999 (tt) cc_final: 0.8733 (pt) REVERT: L 35 GLU cc_start: 0.7809 (tp30) cc_final: 0.7492 (tp30) outliers start: 52 outliers final: 25 residues processed: 404 average time/residue: 0.5053 time to fit residues: 347.8085 Evaluate side-chains 377 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 346 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain P residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 447 optimal weight: 0.6980 chunk 473 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 424 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 559 HIS H 473 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43654 Z= 0.171 Angle : 0.528 9.145 60449 Z= 0.275 Chirality : 0.039 0.216 6958 Planarity : 0.003 0.042 6640 Dihedral : 21.366 161.061 8621 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 1.62 % Allowed : 12.89 % Favored : 85.49 % 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: -0.08 (0.12), residues: 4626 helix: 0.99 (0.12), residues: 2188 sheet: -0.33 (0.19), residues: 673 loop : -1.21 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 712 HIS 0.006 0.001 HIS C 393 PHE 0.019 0.001 PHE G 853 TYR 0.016 0.001 TYR Q 205 ARG 0.007 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 370 time to evaluate : 4.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8044 (t) REVERT: A 129 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: A 137 GLU cc_start: 0.7532 (pm20) cc_final: 0.7273 (pm20) REVERT: B 161 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8315 (pt) REVERT: B 378 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: D 144 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: D 326 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8076 (mmm) REVERT: D 385 ASP cc_start: 0.8051 (t0) cc_final: 0.7743 (t0) REVERT: D 413 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7911 (p) REVERT: F 213 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8043 (tpp80) REVERT: G 775 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6296 (m-80) REVERT: G 858 ASP cc_start: 0.7072 (t0) cc_final: 0.6849 (m-30) REVERT: N 58 LEU cc_start: 0.8600 (tp) cc_final: 0.8339 (tp) REVERT: R 327 GLN cc_start: 0.7133 (mp10) cc_final: 0.6859 (mp10) REVERT: H 504 LYS cc_start: 0.7224 (tttt) cc_final: 0.6965 (ttpp) REVERT: H 555 LYS cc_start: 0.9331 (tmmt) cc_final: 0.9116 (tptt) REVERT: Q 206 ILE cc_start: 0.9002 (tt) cc_final: 0.8752 (pt) REVERT: L 35 GLU cc_start: 0.7743 (tp30) cc_final: 0.7421 (tp30) outliers start: 59 outliers final: 32 residues processed: 409 average time/residue: 0.4959 time to fit residues: 347.1658 Evaluate side-chains 385 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 345 time to evaluate : 4.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 352 optimal weight: 0.1980 chunk 195 optimal weight: 2.9990 chunk 404 optimal weight: 0.3980 chunk 327 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 241 optimal weight: 0.9980 chunk 425 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43654 Z= 0.177 Angle : 0.526 8.904 60449 Z= 0.274 Chirality : 0.039 0.236 6958 Planarity : 0.003 0.040 6640 Dihedral : 21.338 156.343 8621 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 2.12 % Allowed : 13.88 % Favored : 84.00 % 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: 0.03 (0.12), residues: 4626 helix: 1.10 (0.12), residues: 2171 sheet: -0.24 (0.19), residues: 675 loop : -1.18 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 712 HIS 0.003 0.001 HIS K 82 PHE 0.020 0.001 PHE G 853 TYR 0.015 0.001 TYR D 401 ARG 0.007 0.000 ARG M 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 366 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8064 (t) REVERT: A 129 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: A 137 GLU cc_start: 0.7554 (pm20) cc_final: 0.7272 (pm20) REVERT: B 378 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 306 MET cc_start: 0.7390 (ptm) cc_final: 0.7084 (ptp) REVERT: D 144 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6750 (pm20) REVERT: D 326 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8109 (mmm) REVERT: F 213 ARG cc_start: 0.8275 (tpp80) cc_final: 0.8057 (tpp80) REVERT: G 775 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: G 901 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7692 (tmm) REVERT: N 58 LEU cc_start: 0.8596 (tp) cc_final: 0.8344 (tp) REVERT: R 327 GLN cc_start: 0.7189 (mp10) cc_final: 0.6919 (mp10) REVERT: H 46 TRP cc_start: 0.7485 (m100) cc_final: 0.7042 (m100) REVERT: H 225 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7713 (mp) REVERT: H 504 LYS cc_start: 0.7202 (tttt) cc_final: 0.6944 (ttpp) REVERT: H 555 LYS cc_start: 0.9326 (tmmt) cc_final: 0.9111 (tptt) REVERT: Q 206 ILE cc_start: 0.8988 (tt) cc_final: 0.8736 (pt) outliers start: 77 outliers final: 49 residues processed: 418 average time/residue: 0.4981 time to fit residues: 355.0828 Evaluate side-chains 405 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 348 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 532 ASP Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 3.9990 chunk 426 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 278 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 chunk 474 optimal weight: 6.9990 chunk 393 optimal weight: 0.0370 chunk 219 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 156 optimal weight: 0.6980 chunk 248 optimal weight: 0.0070 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 43654 Z= 0.138 Angle : 0.518 11.553 60449 Z= 0.267 Chirality : 0.038 0.270 6958 Planarity : 0.003 0.042 6640 Dihedral : 21.217 154.082 8621 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 1.62 % Allowed : 15.06 % Favored : 83.32 % 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: 0.19 (0.13), residues: 4626 helix: 1.20 (0.12), residues: 2179 sheet: -0.14 (0.19), residues: 676 loop : -1.08 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 712 HIS 0.003 0.000 HIS K 82 PHE 0.015 0.001 PHE G 853 TYR 0.018 0.001 TYR Q 205 ARG 0.007 0.000 ARG M 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 384 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7981 (t) REVERT: A 137 GLU cc_start: 0.7547 (pm20) cc_final: 0.7247 (pm20) REVERT: B 161 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7981 (pt) REVERT: B 378 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 144 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: D 326 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: G 775 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: G 901 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7660 (tmm) REVERT: N 58 LEU cc_start: 0.8565 (tp) cc_final: 0.8346 (tp) REVERT: N 92 ARG cc_start: 0.7572 (ttp80) cc_final: 0.6966 (ttp80) REVERT: H 46 TRP cc_start: 0.7551 (m100) cc_final: 0.7125 (m100) REVERT: H 225 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (mp) REVERT: H 504 LYS cc_start: 0.7097 (tttt) cc_final: 0.6839 (ttpp) REVERT: H 555 LYS cc_start: 0.9328 (tmmt) cc_final: 0.9102 (tptt) REVERT: Q 206 ILE cc_start: 0.8995 (tt) cc_final: 0.8759 (pt) outliers start: 59 outliers final: 32 residues processed: 425 average time/residue: 0.5123 time to fit residues: 373.2157 Evaluate side-chains 390 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 350 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 532 ASP Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 270 optimal weight: 8.9990 chunk 346 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 399 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 472 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 218 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43654 Z= 0.193 Angle : 0.539 11.275 60449 Z= 0.278 Chirality : 0.039 0.265 6958 Planarity : 0.003 0.040 6640 Dihedral : 21.272 152.427 8621 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 1.87 % Allowed : 15.75 % Favored : 82.38 % 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: 0.17 (0.13), residues: 4626 helix: 1.16 (0.12), residues: 2186 sheet: -0.12 (0.19), residues: 675 loop : -1.09 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 932 HIS 0.003 0.001 HIS G1142 PHE 0.019 0.001 PHE G 853 TYR 0.014 0.001 TYR D 401 ARG 0.007 0.000 ARG M 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 354 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8040 (t) REVERT: A 137 GLU cc_start: 0.7568 (pm20) cc_final: 0.7275 (pm20) REVERT: B 161 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8108 (pt) REVERT: B 378 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 278 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 371 MET cc_start: 0.8266 (mmt) cc_final: 0.7843 (mmt) REVERT: D 144 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: D 326 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: D 385 ASP cc_start: 0.8012 (t0) cc_final: 0.7775 (t0) REVERT: E 255 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: G 775 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6238 (m-80) REVERT: G 894 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6734 (mt) REVERT: G 901 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7752 (tmm) REVERT: G 1060 ASP cc_start: 0.7970 (m-30) cc_final: 0.7667 (m-30) REVERT: N 58 LEU cc_start: 0.8586 (tp) cc_final: 0.8367 (tp) REVERT: H 225 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7712 (mp) REVERT: H 504 LYS cc_start: 0.7154 (tttt) cc_final: 0.6906 (ttpp) REVERT: H 555 LYS cc_start: 0.9349 (tmmt) cc_final: 0.9119 (tptt) REVERT: Q 206 ILE cc_start: 0.9062 (tt) cc_final: 0.8800 (pt) REVERT: P 120 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7994 (tttm) outliers start: 68 outliers final: 42 residues processed: 401 average time/residue: 0.4913 time to fit residues: 337.7969 Evaluate side-chains 396 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 344 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 532 ASP Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 233 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 371 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 43654 Z= 0.244 Angle : 0.574 11.041 60449 Z= 0.297 Chirality : 0.040 0.281 6958 Planarity : 0.003 0.039 6640 Dihedral : 21.421 149.169 8621 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 1.92 % Allowed : 16.25 % Favored : 81.83 % 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: 0.02 (0.12), residues: 4626 helix: 1.03 (0.12), residues: 2175 sheet: -0.23 (0.19), residues: 674 loop : -1.11 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 932 HIS 0.004 0.001 HIS A 316 PHE 0.025 0.001 PHE G 853 TYR 0.017 0.001 TYR Q 178 ARG 0.008 0.000 ARG K 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 350 time to evaluate : 4.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8055 (t) REVERT: A 137 GLU cc_start: 0.7649 (pm20) cc_final: 0.7323 (pm20) REVERT: B 161 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 378 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 278 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7659 (tm-30) REVERT: C 371 MET cc_start: 0.8297 (mmt) cc_final: 0.7998 (mmt) REVERT: D 144 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: D 168 MET cc_start: 0.7946 (mmm) cc_final: 0.7445 (ptm) REVERT: D 326 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8116 (mmm) REVERT: E 255 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: G 775 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: G 894 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6740 (mt) REVERT: G 895 ASP cc_start: 0.7487 (t0) cc_final: 0.7147 (t0) REVERT: G 901 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7721 (tmm) REVERT: G 1060 ASP cc_start: 0.8139 (m-30) cc_final: 0.7729 (m-30) REVERT: G 1129 MET cc_start: 0.6770 (mmp) cc_final: 0.6435 (mmm) REVERT: N 58 LEU cc_start: 0.8566 (tp) cc_final: 0.8334 (tp) REVERT: H 225 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7695 (mp) REVERT: H 504 LYS cc_start: 0.7271 (tttt) cc_final: 0.6996 (ttpp) REVERT: H 555 LYS cc_start: 0.9382 (tmmt) cc_final: 0.9163 (tptt) REVERT: Q 206 ILE cc_start: 0.9079 (tt) cc_final: 0.8806 (pt) outliers start: 70 outliers final: 51 residues processed: 400 average time/residue: 0.5039 time to fit residues: 346.6336 Evaluate side-chains 394 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 333 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 532 ASP Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 0.9980 chunk 452 optimal weight: 0.1980 chunk 412 optimal weight: 0.9980 chunk 440 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 345 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 397 optimal weight: 0.9980 chunk 416 optimal weight: 0.8980 chunk 438 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43654 Z= 0.173 Angle : 0.543 11.083 60449 Z= 0.280 Chirality : 0.039 0.293 6958 Planarity : 0.003 0.040 6640 Dihedral : 21.313 147.535 8621 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 16.82 % Favored : 81.64 % 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: 0.17 (0.13), residues: 4626 helix: 1.16 (0.12), residues: 2172 sheet: -0.17 (0.20), residues: 667 loop : -1.03 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 932 HIS 0.004 0.001 HIS E 229 PHE 0.019 0.001 PHE G 853 TYR 0.015 0.001 TYR Q 178 ARG 0.007 0.000 ARG M 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 350 time to evaluate : 4.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7528 (pm20) cc_final: 0.7229 (pm20) REVERT: B 161 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8076 (pt) REVERT: B 378 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 260 MET cc_start: 0.7583 (ttp) cc_final: 0.7208 (ttp) REVERT: C 278 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 144 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: D 168 MET cc_start: 0.7898 (mmm) cc_final: 0.7339 (ptm) REVERT: D 326 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8193 (mmm) REVERT: E 255 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: G 775 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: G 894 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6638 (mt) REVERT: G 901 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7719 (tmm) REVERT: G 1060 ASP cc_start: 0.8127 (m-30) cc_final: 0.7782 (m-30) REVERT: G 1129 MET cc_start: 0.6840 (mmp) cc_final: 0.6532 (mmm) REVERT: N 58 LEU cc_start: 0.8612 (tp) cc_final: 0.8391 (tp) REVERT: H 46 TRP cc_start: 0.7431 (m100) cc_final: 0.7001 (m100) REVERT: H 225 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7692 (mp) REVERT: H 504 LYS cc_start: 0.7178 (tttt) cc_final: 0.6926 (ttpp) REVERT: H 555 LYS cc_start: 0.9369 (tmmt) cc_final: 0.9155 (tptt) REVERT: Q 206 ILE cc_start: 0.9067 (tt) cc_final: 0.8811 (pt) REVERT: P 120 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8002 (tttm) outliers start: 56 outliers final: 42 residues processed: 392 average time/residue: 0.5153 time to fit residues: 345.9471 Evaluate side-chains 390 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 339 time to evaluate : 4.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 532 ASP Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 0.9990 chunk 465 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 323 optimal weight: 30.0000 chunk 488 optimal weight: 6.9990 chunk 449 optimal weight: 0.0070 chunk 388 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 300 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43654 Z= 0.159 Angle : 0.537 11.014 60449 Z= 0.276 Chirality : 0.038 0.299 6958 Planarity : 0.003 0.041 6640 Dihedral : 21.253 146.644 8621 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.59 % Allowed : 16.77 % Favored : 81.64 % 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: 0.27 (0.13), residues: 4626 helix: 1.22 (0.12), residues: 2185 sheet: -0.09 (0.20), residues: 662 loop : -0.99 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 932 HIS 0.004 0.000 HIS E 229 PHE 0.018 0.001 PHE G 853 TYR 0.018 0.001 TYR Q 205 ARG 0.007 0.000 ARG M 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7532 (pm20) cc_final: 0.7236 (pm20) REVERT: B 78 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: B 161 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8062 (pt) REVERT: B 378 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 260 MET cc_start: 0.7479 (ttp) cc_final: 0.7271 (ttp) REVERT: C 278 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7534 (tm-30) REVERT: D 144 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: D 168 MET cc_start: 0.7815 (mmm) cc_final: 0.7290 (ptm) REVERT: D 326 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8193 (mmm) REVERT: D 413 CYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8057 (p) REVERT: E 255 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: G 775 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6289 (m-80) REVERT: G 894 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6597 (mt) REVERT: G 901 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7729 (tmm) REVERT: G 1060 ASP cc_start: 0.8122 (m-30) cc_final: 0.7776 (m-30) REVERT: G 1129 MET cc_start: 0.6828 (mmp) cc_final: 0.6528 (mmm) REVERT: N 58 LEU cc_start: 0.8613 (tp) cc_final: 0.8397 (tp) REVERT: H 46 TRP cc_start: 0.7351 (m100) cc_final: 0.6932 (m100) REVERT: H 225 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7694 (mp) REVERT: H 504 LYS cc_start: 0.7160 (tttt) cc_final: 0.6862 (ttpp) REVERT: H 555 LYS cc_start: 0.9365 (tmmt) cc_final: 0.9147 (tptt) REVERT: Q 206 ILE cc_start: 0.9105 (tt) cc_final: 0.8849 (pt) REVERT: P 120 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8023 (tttm) outliers start: 58 outliers final: 44 residues processed: 397 average time/residue: 0.5205 time to fit residues: 351.0655 Evaluate side-chains 399 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 344 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 532 ASP Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 10.0000 chunk 414 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 chunk 162 optimal weight: 0.4980 chunk 399 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.126416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097841 restraints weight = 88251.829| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.42 r_work: 0.3542 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43654 Z= 0.164 Angle : 0.539 11.037 60449 Z= 0.277 Chirality : 0.038 0.299 6958 Planarity : 0.003 0.054 6640 Dihedral : 21.236 145.750 8621 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 1.73 % Allowed : 16.85 % Favored : 81.42 % 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: 0.30 (0.13), residues: 4626 helix: 1.25 (0.12), residues: 2178 sheet: -0.09 (0.20), residues: 666 loop : -0.95 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 932 HIS 0.003 0.000 HIS K 82 PHE 0.022 0.001 PHE M 78 TYR 0.015 0.001 TYR Q 178 ARG 0.014 0.000 ARG Q 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8870.34 seconds wall clock time: 161 minutes 18.11 seconds (9678.11 seconds total)