Starting phenix.real_space_refine on Sat Feb 7 17:17:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k2v_36840/02_2026/8k2v_36840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k2v_36840/02_2026/8k2v_36840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k2v_36840/02_2026/8k2v_36840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k2v_36840/02_2026/8k2v_36840_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k2v_36840/02_2026/8k2v_36840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k2v_36840/02_2026/8k2v_36840.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 192 5.16 5 C 22224 2.51 5 N 6054 2.21 5 O 6714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35202 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "B" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "D" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "E" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain: "G" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "I" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "J" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "K" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "L" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "H" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.96, per 1000 atoms: 0.23 Number of scatterers: 35202 At special positions: 0 Unit cell: (158.86, 150.4, 147.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 192 16.00 P 18 15.00 O 6714 8.00 N 6054 7.00 C 22224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 41.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 504 through 530 removed outlier: 3.643A pdb=" N ILE A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 639 through 645 removed outlier: 3.574A pdb=" N GLN A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 530 removed outlier: 3.643A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 639 through 645 removed outlier: 3.574A pdb=" N GLN B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 530 removed outlier: 3.643A pdb=" N ILE C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 639 through 645 removed outlier: 3.574A pdb=" N GLN C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 530 removed outlier: 3.643A pdb=" N ILE D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 639 through 645 removed outlier: 3.574A pdb=" N GLN D 643 " --> pdb=" O SER D 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 530 removed outlier: 3.642A pdb=" N ILE E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 639 through 645 removed outlier: 3.573A pdb=" N GLN E 643 " --> pdb=" O SER E 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 530 removed outlier: 3.643A pdb=" N ILE F 516 " --> pdb=" O ALA F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 539 Processing helix chain 'F' and resid 639 through 645 removed outlier: 3.574A pdb=" N GLN F 643 " --> pdb=" O SER F 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 65 Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 114 through 117 Processing helix chain 'G' and resid 140 through 144 Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 192 through 204 removed outlier: 3.523A pdb=" N TYR G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 227 removed outlier: 3.882A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 Processing helix chain 'G' and resid 256 through 261 removed outlier: 3.599A pdb=" N LEU G 260 " --> pdb=" O SER G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 269 removed outlier: 3.602A pdb=" N LYS G 269 " --> pdb=" O LEU G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 294 Processing helix chain 'G' and resid 315 through 322 removed outlier: 4.365A pdb=" N GLY G 319 " --> pdb=" O ASP G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 339 removed outlier: 4.108A pdb=" N VAL G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 377 through 395 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 417 through 432 Processing helix chain 'G' and resid 447 through 452 Processing helix chain 'G' and resid 454 through 458 Processing helix chain 'G' and resid 474 through 493 Processing helix chain 'G' and resid 501 through 518 Proline residue: G 508 - end of helix removed outlier: 3.509A pdb=" N ASN G 518 " --> pdb=" O GLU G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 525 removed outlier: 3.679A pdb=" N ARG G 525 " --> pdb=" O TYR G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 549 Processing helix chain 'I' and resid 39 through 65 Processing helix chain 'I' and resid 68 through 78 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 114 through 117 Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'I' and resid 146 through 164 Processing helix chain 'I' and resid 192 through 204 removed outlier: 3.522A pdb=" N TYR I 196 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 227 removed outlier: 3.882A pdb=" N ALA I 225 " --> pdb=" O ALA I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 252 Processing helix chain 'I' and resid 256 through 261 removed outlier: 3.599A pdb=" N LEU I 260 " --> pdb=" O SER I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 269 removed outlier: 3.602A pdb=" N LYS I 269 " --> pdb=" O LEU I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 294 Processing helix chain 'I' and resid 315 through 322 removed outlier: 4.365A pdb=" N GLY I 319 " --> pdb=" O ASP I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 339 removed outlier: 4.107A pdb=" N VAL I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 377 through 395 Processing helix chain 'I' and resid 410 through 416 Processing helix chain 'I' and resid 417 through 432 Processing helix chain 'I' and resid 447 through 452 Processing helix chain 'I' and resid 454 through 458 Processing helix chain 'I' and resid 474 through 493 Processing helix chain 'I' and resid 501 through 518 Proline residue: I 508 - end of helix removed outlier: 3.509A pdb=" N ASN I 518 " --> pdb=" O GLU I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 525 removed outlier: 3.679A pdb=" N ARG I 525 " --> pdb=" O TYR I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 535 No H-bonds generated for 'chain 'I' and resid 533 through 535' Processing helix chain 'I' and resid 536 through 549 Processing helix chain 'J' and resid 39 through 65 Processing helix chain 'J' and resid 68 through 78 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 192 through 204 removed outlier: 3.523A pdb=" N TYR J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 removed outlier: 3.881A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 252 Processing helix chain 'J' and resid 256 through 261 removed outlier: 3.600A pdb=" N LEU J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 269 removed outlier: 3.603A pdb=" N LYS J 269 " --> pdb=" O LEU J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 294 Processing helix chain 'J' and resid 315 through 322 removed outlier: 4.366A pdb=" N GLY J 319 " --> pdb=" O ASP J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 339 removed outlier: 4.107A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 343 Processing helix chain 'J' and resid 377 through 395 Processing helix chain 'J' and resid 410 through 416 Processing helix chain 'J' and resid 417 through 432 Processing helix chain 'J' and resid 447 through 452 Processing helix chain 'J' and resid 454 through 458 Processing helix chain 'J' and resid 474 through 493 Processing helix chain 'J' and resid 501 through 518 Proline residue: J 508 - end of helix removed outlier: 3.509A pdb=" N ASN J 518 " --> pdb=" O GLU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.680A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 39 through 65 Processing helix chain 'K' and resid 68 through 78 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 114 through 117 Processing helix chain 'K' and resid 140 through 144 Processing helix chain 'K' and resid 146 through 164 Processing helix chain 'K' and resid 192 through 204 removed outlier: 3.522A pdb=" N TYR K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 227 removed outlier: 3.882A pdb=" N ALA K 225 " --> pdb=" O ALA K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 252 Processing helix chain 'K' and resid 256 through 261 removed outlier: 3.599A pdb=" N LEU K 260 " --> pdb=" O SER K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 269 removed outlier: 3.603A pdb=" N LYS K 269 " --> pdb=" O LEU K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 294 Processing helix chain 'K' and resid 315 through 322 removed outlier: 4.365A pdb=" N GLY K 319 " --> pdb=" O ASP K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 339 removed outlier: 4.107A pdb=" N VAL K 334 " --> pdb=" O ASP K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 343 Processing helix chain 'K' and resid 377 through 395 Processing helix chain 'K' and resid 410 through 416 Processing helix chain 'K' and resid 417 through 432 Processing helix chain 'K' and resid 447 through 452 Processing helix chain 'K' and resid 454 through 458 Processing helix chain 'K' and resid 474 through 493 Processing helix chain 'K' and resid 501 through 518 Proline residue: K 508 - end of helix removed outlier: 3.510A pdb=" N ASN K 518 " --> pdb=" O GLU K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 518 through 525 removed outlier: 3.679A pdb=" N ARG K 525 " --> pdb=" O TYR K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 533 through 535 No H-bonds generated for 'chain 'K' and resid 533 through 535' Processing helix chain 'K' and resid 536 through 549 Processing helix chain 'L' and resid 39 through 65 Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'L' and resid 140 through 144 Processing helix chain 'L' and resid 146 through 164 Processing helix chain 'L' and resid 192 through 204 removed outlier: 3.522A pdb=" N TYR L 196 " --> pdb=" O GLY L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 227 removed outlier: 3.882A pdb=" N ALA L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 252 Processing helix chain 'L' and resid 256 through 261 removed outlier: 3.600A pdb=" N LEU L 260 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 269 removed outlier: 3.602A pdb=" N LYS L 269 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 294 Processing helix chain 'L' and resid 315 through 322 removed outlier: 4.364A pdb=" N GLY L 319 " --> pdb=" O ASP L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 339 removed outlier: 4.107A pdb=" N VAL L 334 " --> pdb=" O ASP L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 343 Processing helix chain 'L' and resid 377 through 395 Processing helix chain 'L' and resid 410 through 416 Processing helix chain 'L' and resid 417 through 432 Processing helix chain 'L' and resid 447 through 452 Processing helix chain 'L' and resid 454 through 458 Processing helix chain 'L' and resid 474 through 493 Processing helix chain 'L' and resid 501 through 518 Proline residue: L 508 - end of helix removed outlier: 3.508A pdb=" N ASN L 518 " --> pdb=" O GLU L 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.679A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 535 No H-bonds generated for 'chain 'L' and resid 533 through 535' Processing helix chain 'L' and resid 536 through 549 Processing helix chain 'H' and resid 39 through 65 Processing helix chain 'H' and resid 68 through 78 Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 114 through 117 Processing helix chain 'H' and resid 140 through 144 Processing helix chain 'H' and resid 146 through 164 Processing helix chain 'H' and resid 192 through 204 removed outlier: 3.522A pdb=" N TYR H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 removed outlier: 3.881A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 252 Processing helix chain 'H' and resid 256 through 261 removed outlier: 3.599A pdb=" N LEU H 260 " --> pdb=" O SER H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 269 removed outlier: 3.602A pdb=" N LYS H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 294 Processing helix chain 'H' and resid 315 through 322 removed outlier: 4.365A pdb=" N GLY H 319 " --> pdb=" O ASP H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 339 removed outlier: 4.108A pdb=" N VAL H 334 " --> pdb=" O ASP H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 377 through 395 Processing helix chain 'H' and resid 410 through 416 Processing helix chain 'H' and resid 417 through 432 Processing helix chain 'H' and resid 447 through 452 Processing helix chain 'H' and resid 454 through 458 Processing helix chain 'H' and resid 474 through 493 Processing helix chain 'H' and resid 501 through 518 Proline residue: H 508 - end of helix removed outlier: 3.509A pdb=" N ASN H 518 " --> pdb=" O GLU H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 525 removed outlier: 3.679A pdb=" N ARG H 525 " --> pdb=" O TYR H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 535 No H-bonds generated for 'chain 'H' and resid 533 through 535' Processing helix chain 'H' and resid 536 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 550 through 557 removed outlier: 3.574A pdb=" N ALA A 565 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 575 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 612 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 656 through 660 removed outlier: 7.230A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL A 660 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A 674 " --> pdb=" O VAL A 660 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 694 through 697 Processing sheet with id=AA4, first strand: chain 'B' and resid 550 through 557 removed outlier: 3.574A pdb=" N ALA B 565 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 575 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 612 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 656 through 660 removed outlier: 7.230A pdb=" N VAL B 676 " --> pdb=" O GLU B 658 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL B 660 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU B 674 " --> pdb=" O VAL B 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 694 through 697 Processing sheet with id=AA7, first strand: chain 'C' and resid 550 through 557 removed outlier: 3.573A pdb=" N ALA C 565 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 575 " --> pdb=" O THR C 567 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 612 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 656 through 660 removed outlier: 7.230A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL C 660 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 674 " --> pdb=" O VAL C 660 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 694 through 697 Processing sheet with id=AB1, first strand: chain 'D' and resid 550 through 557 removed outlier: 3.574A pdb=" N ALA D 565 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER D 575 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR D 596 " --> pdb=" O LEU D 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 612 " --> pdb=" O TYR D 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 656 through 660 removed outlier: 7.229A pdb=" N VAL D 676 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL D 660 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU D 674 " --> pdb=" O VAL D 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 694 through 697 Processing sheet with id=AB4, first strand: chain 'E' and resid 550 through 557 removed outlier: 3.574A pdb=" N ALA E 565 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 575 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 612 " --> pdb=" O TYR E 619 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 656 through 660 removed outlier: 7.230A pdb=" N VAL E 676 " --> pdb=" O GLU E 658 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL E 660 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU E 674 " --> pdb=" O VAL E 660 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 694 through 697 Processing sheet with id=AB7, first strand: chain 'F' and resid 550 through 557 removed outlier: 3.574A pdb=" N ALA F 565 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 575 " --> pdb=" O THR F 567 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR F 596 " --> pdb=" O LEU F 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 612 " --> pdb=" O TYR F 619 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 656 through 660 removed outlier: 7.230A pdb=" N VAL F 676 " --> pdb=" O GLU F 658 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL F 660 " --> pdb=" O LEU F 674 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU F 674 " --> pdb=" O VAL F 660 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 694 through 697 Processing sheet with id=AC1, first strand: chain 'G' and resid 98 through 99 removed outlier: 8.498A pdb=" N ILE G 168 " --> pdb=" O GLU G 130 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET G 132 " --> pdb=" O ILE G 168 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU G 170 " --> pdb=" O MET G 132 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE G 134 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU G 229 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN G 230 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA G 277 " --> pdb=" O ASN G 230 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE G 232 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 215 through 217 removed outlier: 3.877A pdb=" N PHE G 240 " --> pdb=" O CYS G 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 345 through 346 removed outlier: 3.506A pdb=" N THR G 345 " --> pdb=" O PHE G 359 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE G 359 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU G 399 " --> pdb=" O PRO G 366 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY G 368 " --> pdb=" O LEU G 399 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU G 401 " --> pdb=" O GLY G 368 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 370 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU G 398 " --> pdb=" O ILE G 437 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU G 439 " --> pdb=" O LEU G 398 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE G 400 " --> pdb=" O LEU G 439 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE G 461 " --> pdb=" O LYS G 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 438 " --> pdb=" O PHE G 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY G 530 " --> pdb=" O LEU G 462 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 98 through 99 removed outlier: 8.498A pdb=" N ILE I 168 " --> pdb=" O GLU I 130 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET I 132 " --> pdb=" O ILE I 168 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU I 170 " --> pdb=" O MET I 132 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE I 134 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU I 229 " --> pdb=" O GLN I 208 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN I 230 " --> pdb=" O HIS I 275 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA I 277 " --> pdb=" O ASN I 230 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE I 232 " --> pdb=" O ALA I 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 215 through 217 removed outlier: 3.876A pdb=" N PHE I 240 " --> pdb=" O CYS I 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 345 through 346 removed outlier: 3.506A pdb=" N THR I 345 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE I 359 " --> pdb=" O THR I 345 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU I 399 " --> pdb=" O PRO I 366 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY I 368 " --> pdb=" O LEU I 399 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU I 401 " --> pdb=" O GLY I 368 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL I 370 " --> pdb=" O LEU I 401 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU I 398 " --> pdb=" O ILE I 437 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU I 439 " --> pdb=" O LEU I 398 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE I 400 " --> pdb=" O LEU I 439 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE I 461 " --> pdb=" O LYS I 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR I 438 " --> pdb=" O PHE I 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY I 530 " --> pdb=" O LEU I 462 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 98 through 99 removed outlier: 8.498A pdb=" N ILE J 168 " --> pdb=" O GLU J 130 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET J 132 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU J 170 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE J 134 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU J 229 " --> pdb=" O GLN J 208 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 215 through 217 removed outlier: 3.877A pdb=" N PHE J 240 " --> pdb=" O CYS J 216 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 345 through 346 removed outlier: 3.506A pdb=" N THR J 345 " --> pdb=" O PHE J 359 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 359 " --> pdb=" O THR J 345 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU J 398 " --> pdb=" O ILE J 437 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU J 439 " --> pdb=" O LEU J 398 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE J 400 " --> pdb=" O LEU J 439 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR J 438 " --> pdb=" O PHE J 461 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY J 530 " --> pdb=" O LEU J 462 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 98 through 99 removed outlier: 8.499A pdb=" N ILE K 168 " --> pdb=" O GLU K 130 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET K 132 " --> pdb=" O ILE K 168 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU K 170 " --> pdb=" O MET K 132 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE K 134 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU K 229 " --> pdb=" O GLN K 208 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN K 230 " --> pdb=" O HIS K 275 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA K 277 " --> pdb=" O ASN K 230 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE K 232 " --> pdb=" O ALA K 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 215 through 217 removed outlier: 3.877A pdb=" N PHE K 240 " --> pdb=" O CYS K 216 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 345 through 346 removed outlier: 3.506A pdb=" N THR K 345 " --> pdb=" O PHE K 359 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE K 359 " --> pdb=" O THR K 345 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU K 399 " --> pdb=" O PRO K 366 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY K 368 " --> pdb=" O LEU K 399 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU K 401 " --> pdb=" O GLY K 368 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL K 370 " --> pdb=" O LEU K 401 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU K 398 " --> pdb=" O ILE K 437 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU K 439 " --> pdb=" O LEU K 398 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE K 400 " --> pdb=" O LEU K 439 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE K 461 " --> pdb=" O LYS K 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR K 438 " --> pdb=" O PHE K 461 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY K 530 " --> pdb=" O LEU K 462 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 98 through 99 removed outlier: 8.499A pdb=" N ILE L 168 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET L 132 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU L 170 " --> pdb=" O MET L 132 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE L 134 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU L 229 " --> pdb=" O GLN L 208 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN L 230 " --> pdb=" O HIS L 275 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 215 through 217 removed outlier: 3.877A pdb=" N PHE L 240 " --> pdb=" O CYS L 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 345 through 346 removed outlier: 3.506A pdb=" N THR L 345 " --> pdb=" O PHE L 359 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE L 359 " --> pdb=" O THR L 345 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU L 398 " --> pdb=" O ILE L 437 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU L 439 " --> pdb=" O LEU L 398 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE L 400 " --> pdb=" O LEU L 439 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR L 438 " --> pdb=" O PHE L 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY L 530 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 98 through 99 removed outlier: 8.499A pdb=" N ILE H 168 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET H 132 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU H 170 " --> pdb=" O MET H 132 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE H 134 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 229 " --> pdb=" O GLN H 208 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 215 through 217 removed outlier: 3.877A pdb=" N PHE H 240 " --> pdb=" O CYS H 216 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 345 through 346 removed outlier: 3.506A pdb=" N THR H 345 " --> pdb=" O PHE H 359 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE H 359 " --> pdb=" O THR H 345 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU H 399 " --> pdb=" O PRO H 366 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU H 398 " --> pdb=" O ILE H 437 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU H 439 " --> pdb=" O LEU H 398 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE H 400 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR H 438 " --> pdb=" O PHE H 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY H 530 " --> pdb=" O LEU H 462 " (cutoff:3.500A) 1631 hydrogen bonds defined for protein. 4590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11639 1.34 - 1.46: 7681 1.46 - 1.58: 16218 1.58 - 1.70: 36 1.70 - 1.83: 312 Bond restraints: 35886 Sorted by residual: bond pdb=" C5A ACO K 601 " pdb=" C6A ACO K 601 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.16e+01 bond pdb=" C5A ACO H 601 " pdb=" C6A ACO H 601 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C4A ACO J 601 " pdb=" C5A ACO J 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.20e-02 6.94e+03 4.58e+01 bond pdb=" C4A ACO H 601 " pdb=" C5A ACO H 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.20e-02 6.94e+03 4.54e+01 bond pdb=" C5A ACO L 601 " pdb=" C6A ACO L 601 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.53e+01 ... (remaining 35881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 48274 3.95 - 7.91: 196 7.91 - 11.86: 21 11.86 - 15.82: 13 15.82 - 19.77: 6 Bond angle restraints: 48510 Sorted by residual: angle pdb=" P1A ACO K 601 " pdb=" O3A ACO K 601 " pdb=" P2A ACO K 601 " ideal model delta sigma weight residual 136.83 119.86 16.97 1.00e+00 1.00e+00 2.88e+02 angle pdb=" P1A ACO J 601 " pdb=" O3A ACO J 601 " pdb=" P2A ACO J 601 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" P1A ACO I 601 " pdb=" O3A ACO I 601 " pdb=" P2A ACO I 601 " ideal model delta sigma weight residual 136.83 120.66 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" P1A ACO L 601 " pdb=" O3A ACO L 601 " pdb=" P2A ACO L 601 " ideal model delta sigma weight residual 136.83 120.75 16.08 1.00e+00 1.00e+00 2.58e+02 angle pdb=" P1A ACO G 601 " pdb=" O3A ACO G 601 " pdb=" P2A ACO G 601 " ideal model delta sigma weight residual 136.83 120.76 16.07 1.00e+00 1.00e+00 2.58e+02 ... (remaining 48505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.13: 19704 19.13 - 38.26: 1721 38.26 - 57.38: 276 57.38 - 76.51: 70 76.51 - 95.64: 27 Dihedral angle restraints: 21798 sinusoidal: 8892 harmonic: 12906 Sorted by residual: dihedral pdb=" N ASP F 580 " pdb=" C ASP F 580 " pdb=" CA ASP F 580 " pdb=" CB ASP F 580 " ideal model delta harmonic sigma weight residual 122.80 133.93 -11.13 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" C ASP F 580 " pdb=" N ASP F 580 " pdb=" CA ASP F 580 " pdb=" CB ASP F 580 " ideal model delta harmonic sigma weight residual -122.60 -133.60 11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" CA PHE G 185 " pdb=" C PHE G 185 " pdb=" N PRO G 186 " pdb=" CA PRO G 186 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 21795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4770 0.081 - 0.162: 548 0.162 - 0.243: 21 0.243 - 0.324: 0 0.324 - 0.406: 1 Chirality restraints: 5340 Sorted by residual: chirality pdb=" CA ASP F 580 " pdb=" N ASP F 580 " pdb=" C ASP F 580 " pdb=" CB ASP F 580 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA ASN F 560 " pdb=" N ASN F 560 " pdb=" C ASN F 560 " pdb=" CB ASN F 560 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASN A 560 " pdb=" N ASN A 560 " pdb=" C ASN A 560 " pdb=" CB ASN A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5337 not shown) Planarity restraints: 6294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO L 601 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.14e+03 pdb=" C5P ACO L 601 " -0.083 2.00e-02 2.50e+03 pdb=" C6P ACO L 601 " 0.088 2.00e-02 2.50e+03 pdb=" N4P ACO L 601 " -0.534 2.00e-02 2.50e+03 pdb=" O5P ACO L 601 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO J 601 " 0.344 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C5P ACO J 601 " -0.089 2.00e-02 2.50e+03 pdb=" C6P ACO J 601 " 0.174 2.00e-02 2.50e+03 pdb=" N4P ACO J 601 " -0.511 2.00e-02 2.50e+03 pdb=" O5P ACO J 601 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO K 601 " -0.328 2.00e-02 2.50e+03 2.78e-01 9.66e+02 pdb=" C5P ACO K 601 " 0.084 2.00e-02 2.50e+03 pdb=" C6P ACO K 601 " -0.177 2.00e-02 2.50e+03 pdb=" N4P ACO K 601 " 0.486 2.00e-02 2.50e+03 pdb=" O5P ACO K 601 " -0.064 2.00e-02 2.50e+03 ... (remaining 6291 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5539 2.76 - 3.29: 36151 3.29 - 3.83: 58022 3.83 - 4.36: 69556 4.36 - 4.90: 117272 Nonbonded interactions: 286540 Sorted by model distance: nonbonded pdb=" O GLY J 174 " pdb=" OG1 THR J 217 " model vdw 2.222 3.040 nonbonded pdb=" O GLY G 174 " pdb=" OG1 THR G 217 " model vdw 2.223 3.040 nonbonded pdb=" O GLY K 174 " pdb=" OG1 THR K 217 " model vdw 2.223 3.040 nonbonded pdb=" O GLY H 174 " pdb=" OG1 THR H 217 " model vdw 2.223 3.040 nonbonded pdb=" O GLY L 174 " pdb=" OG1 THR L 217 " model vdw 2.223 3.040 ... (remaining 286535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 32.440 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.005 0.105 35892 Z= 0.297 Angle : 0.751 19.771 48510 Z= 0.459 Chirality : 0.045 0.406 5340 Planarity : 0.011 0.301 6294 Dihedral : 14.806 95.640 13590 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.44 % Allowed : 1.63 % Favored : 96.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4506 helix: 1.59 (0.13), residues: 1656 sheet: 0.71 (0.17), residues: 750 loop : -0.65 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 543 TYR 0.020 0.001 TYR F 619 PHE 0.011 0.001 PHE J 240 TRP 0.004 0.001 TRP L 276 HIS 0.002 0.001 HIS H 275 Details of bonding type rmsd covalent geometry : bond 0.00490 (35886) covalent geometry : angle 0.75068 (48510) hydrogen bonds : bond 0.21253 ( 1631) hydrogen bonds : angle 7.88213 ( 4590) Misc. bond : bond 0.03416 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 285 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.9006 (tmm) cc_final: 0.8769 (tmm) REVERT: A 616 ASN cc_start: 0.8090 (m-40) cc_final: 0.7819 (m-40) REVERT: B 509 CYS cc_start: 0.9164 (m) cc_final: 0.8805 (m) REVERT: B 553 MET cc_start: 0.8023 (mtt) cc_final: 0.7812 (mmm) REVERT: B 600 CYS cc_start: 0.8730 (p) cc_final: 0.8288 (p) REVERT: C 522 MET cc_start: 0.8784 (tmm) cc_final: 0.8570 (tmm) REVERT: D 600 CYS cc_start: 0.8508 (p) cc_final: 0.8123 (p) REVERT: F 522 MET cc_start: 0.8660 (tmm) cc_final: 0.8380 (tmm) REVERT: F 682 MET cc_start: 0.2045 (tpt) cc_final: 0.1411 (ttm) REVERT: G 213 MET cc_start: 0.8068 (mpp) cc_final: 0.7641 (mpp) REVERT: I 213 MET cc_start: 0.8264 (mpp) cc_final: 0.7797 (mpp) REVERT: J 408 MET cc_start: 0.4790 (ptp) cc_final: 0.4434 (ptp) REVERT: K 213 MET cc_start: 0.8241 (mpp) cc_final: 0.7831 (mpp) REVERT: L 213 MET cc_start: 0.8060 (mpp) cc_final: 0.7640 (mpp) REVERT: L 452 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8968 (mtp) REVERT: H 213 MET cc_start: 0.8223 (mpp) cc_final: 0.7806 (mpp) outliers start: 53 outliers final: 10 residues processed: 305 average time/residue: 0.2075 time to fit residues: 105.5240 Evaluate side-chains 254 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain F residue 543 ARG Chi-restraints excluded: chain F residue 556 LYS Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 452 MET Chi-restraints excluded: chain L residue 452 MET Chi-restraints excluded: chain H residue 452 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 560 ASN A 570 HIS B 510 GLN B 616 ASN D 510 GLN D 560 ASN F 510 GLN F 570 HIS G 102 GLN G 402 GLN G 433 GLN I 102 GLN ** I 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 433 GLN J 102 GLN ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN K 102 GLN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 433 GLN L 102 GLN ** L 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 433 GLN H 102 GLN H 389 GLN ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066156 restraints weight = 168841.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067543 restraints weight = 97468.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068397 restraints weight = 71523.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068745 restraints weight = 59537.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069098 restraints weight = 54650.966| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 35892 Z= 0.266 Angle : 0.646 8.533 48510 Z= 0.343 Chirality : 0.046 0.184 5340 Planarity : 0.004 0.056 6294 Dihedral : 9.750 86.035 5386 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.27 % Allowed : 7.27 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 4506 helix: 1.80 (0.13), residues: 1656 sheet: 1.02 (0.18), residues: 738 loop : -0.60 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 327 TYR 0.024 0.002 TYR C 590 PHE 0.017 0.002 PHE L 240 TRP 0.007 0.001 TRP G 276 HIS 0.006 0.001 HIS L 266 Details of bonding type rmsd covalent geometry : bond 0.00573 (35886) covalent geometry : angle 0.64614 (48510) hydrogen bonds : bond 0.05583 ( 1631) hydrogen bonds : angle 5.80929 ( 4590) Misc. bond : bond 0.00060 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8708 (tmm) cc_final: 0.8430 (tmm) REVERT: A 553 MET cc_start: 0.8768 (mmm) cc_final: 0.8483 (mmm) REVERT: C 522 MET cc_start: 0.8580 (tmm) cc_final: 0.8263 (tmm) REVERT: C 524 ASP cc_start: 0.8766 (m-30) cc_final: 0.8548 (t0) REVERT: C 551 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7665 (ttt180) REVERT: C 682 MET cc_start: 0.3942 (mmm) cc_final: 0.3313 (mmt) REVERT: D 551 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8478 (tmm-80) REVERT: D 600 CYS cc_start: 0.8961 (p) cc_final: 0.8578 (p) REVERT: E 522 MET cc_start: 0.8608 (tmm) cc_final: 0.8318 (tmm) REVERT: E 524 ASP cc_start: 0.8856 (m-30) cc_final: 0.8447 (t0) REVERT: E 616 ASN cc_start: 0.8197 (m-40) cc_final: 0.7986 (m-40) REVERT: F 522 MET cc_start: 0.8207 (tmm) cc_final: 0.7649 (tmm) REVERT: F 534 PHE cc_start: 0.9164 (m-80) cc_final: 0.8880 (m-80) REVERT: G 425 MET cc_start: 0.9042 (mmm) cc_final: 0.8632 (tpp) REVERT: I 425 MET cc_start: 0.9062 (mmm) cc_final: 0.8770 (tpp) REVERT: J 408 MET cc_start: 0.4680 (ptp) cc_final: 0.4478 (ptp) outliers start: 10 outliers final: 0 residues processed: 255 average time/residue: 0.2008 time to fit residues: 87.3468 Evaluate side-chains 239 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 551 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 254 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 397 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 242 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 570 HIS B 510 GLN B 616 ASN C 570 HIS D 560 ASN G 496 GLN ** I 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 496 GLN ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 GLN ** L 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 496 GLN H 402 GLN H 496 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066988 restraints weight = 164865.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068365 restraints weight = 96627.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.069216 restraints weight = 70939.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069572 restraints weight = 59521.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069959 restraints weight = 54556.383| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35892 Z= 0.141 Angle : 0.534 8.694 48510 Z= 0.280 Chirality : 0.044 0.168 5340 Planarity : 0.003 0.049 6294 Dihedral : 9.074 76.361 5346 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.79 % Allowed : 8.88 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4506 helix: 2.16 (0.13), residues: 1656 sheet: 0.51 (0.17), residues: 870 loop : -0.48 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 327 TYR 0.024 0.001 TYR C 590 PHE 0.014 0.001 PHE H 240 TRP 0.007 0.001 TRP I 276 HIS 0.003 0.001 HIS H 266 Details of bonding type rmsd covalent geometry : bond 0.00302 (35886) covalent geometry : angle 0.53438 (48510) hydrogen bonds : bond 0.04531 ( 1631) hydrogen bonds : angle 5.13015 ( 4590) Misc. bond : bond 0.00015 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8798 (tmm) cc_final: 0.8439 (tmm) REVERT: A 682 MET cc_start: 0.5258 (tpt) cc_final: 0.5011 (tpp) REVERT: B 534 PHE cc_start: 0.9075 (m-80) cc_final: 0.8785 (m-80) REVERT: B 677 MET cc_start: 0.3411 (ttp) cc_final: 0.1642 (ttp) REVERT: C 522 MET cc_start: 0.8749 (tmm) cc_final: 0.8385 (tmm) REVERT: C 524 ASP cc_start: 0.8695 (m-30) cc_final: 0.8467 (t0) REVERT: C 682 MET cc_start: 0.4247 (mmm) cc_final: 0.3862 (mmt) REVERT: D 522 MET cc_start: 0.8111 (tmm) cc_final: 0.7726 (tmm) REVERT: D 600 CYS cc_start: 0.9020 (p) cc_final: 0.8609 (p) REVERT: E 522 MET cc_start: 0.8687 (tmm) cc_final: 0.8206 (tmm) REVERT: E 524 ASP cc_start: 0.8855 (m-30) cc_final: 0.8512 (t0) REVERT: F 522 MET cc_start: 0.8336 (tmm) cc_final: 0.7579 (tmm) REVERT: G 213 MET cc_start: 0.7975 (mpp) cc_final: 0.7677 (mpp) REVERT: I 213 MET cc_start: 0.8033 (mpp) cc_final: 0.7811 (mpp) REVERT: L 425 MET cc_start: 0.9003 (tpp) cc_final: 0.8510 (tpp) REVERT: H 213 MET cc_start: 0.8057 (mpp) cc_final: 0.7741 (mpp) REVERT: H 408 MET cc_start: 0.4639 (OUTLIER) cc_final: 0.4299 (ptp) outliers start: 29 outliers final: 9 residues processed: 264 average time/residue: 0.1905 time to fit residues: 86.4283 Evaluate side-chains 245 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain G residue 526 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain K residue 526 VAL Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain H residue 408 MET Chi-restraints excluded: chain H residue 526 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 310 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 415 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 149 optimal weight: 0.0980 chunk 123 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 chunk 145 optimal weight: 0.0000 chunk 209 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN C 584 GLN D 616 ASN E 510 GLN I 402 GLN ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 402 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.085403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.067729 restraints weight = 164988.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069196 restraints weight = 94437.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069947 restraints weight = 68728.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070526 restraints weight = 57748.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.070836 restraints weight = 51672.464| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35892 Z= 0.102 Angle : 0.511 9.233 48510 Z= 0.265 Chirality : 0.043 0.162 5340 Planarity : 0.003 0.043 6294 Dihedral : 8.770 84.036 5346 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.03 % Allowed : 9.85 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4506 helix: 2.35 (0.13), residues: 1656 sheet: 0.68 (0.18), residues: 804 loop : -0.43 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 327 TYR 0.022 0.001 TYR C 590 PHE 0.022 0.001 PHE E 526 TRP 0.006 0.001 TRP I 276 HIS 0.008 0.001 HIS C 684 Details of bonding type rmsd covalent geometry : bond 0.00217 (35886) covalent geometry : angle 0.51055 (48510) hydrogen bonds : bond 0.03627 ( 1631) hydrogen bonds : angle 4.71095 ( 4590) Misc. bond : bond 0.00010 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8798 (tmm) cc_final: 0.8182 (tmm) REVERT: C 522 MET cc_start: 0.8707 (tmm) cc_final: 0.8138 (tmm) REVERT: C 613 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8673 (mt) REVERT: C 682 MET cc_start: 0.4114 (mmm) cc_final: 0.3855 (mmt) REVERT: D 522 MET cc_start: 0.8050 (tmm) cc_final: 0.7617 (tmm) REVERT: D 600 CYS cc_start: 0.9000 (p) cc_final: 0.8581 (p) REVERT: E 522 MET cc_start: 0.8725 (tmm) cc_final: 0.8202 (tmm) REVERT: E 524 ASP cc_start: 0.8842 (m-30) cc_final: 0.8395 (t0) REVERT: F 522 MET cc_start: 0.8364 (tmm) cc_final: 0.7874 (tmm) REVERT: F 534 PHE cc_start: 0.9212 (m-80) cc_final: 0.8966 (m-80) REVERT: G 408 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.3748 (ptp) REVERT: I 201 MET cc_start: 0.8691 (mtt) cc_final: 0.8469 (mtt) REVERT: L 425 MET cc_start: 0.9008 (tpp) cc_final: 0.8493 (tpp) REVERT: H 213 MET cc_start: 0.8144 (mpp) cc_final: 0.7893 (mpp) REVERT: H 408 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.4335 (ptp) outliers start: 38 outliers final: 5 residues processed: 268 average time/residue: 0.1902 time to fit residues: 89.0122 Evaluate side-chains 240 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain C residue 509 CYS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain G residue 408 MET Chi-restraints excluded: chain H residue 408 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 403 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 413 optimal weight: 0.9990 chunk 425 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 445 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 684 HIS B 616 ASN D 616 ASN D 684 HIS E 510 GLN E 616 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 372 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.085514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067760 restraints weight = 162587.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069031 restraints weight = 98259.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069768 restraints weight = 72719.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069953 restraints weight = 62535.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070433 restraints weight = 58834.416| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35892 Z= 0.139 Angle : 0.519 12.108 48510 Z= 0.268 Chirality : 0.043 0.168 5340 Planarity : 0.003 0.040 6294 Dihedral : 8.656 87.784 5346 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.68 % Allowed : 11.26 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4506 helix: 2.41 (0.13), residues: 1656 sheet: 0.86 (0.18), residues: 786 loop : -0.46 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 551 TYR 0.024 0.001 TYR C 590 PHE 0.009 0.001 PHE H 240 TRP 0.005 0.001 TRP L 276 HIS 0.002 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00305 (35886) covalent geometry : angle 0.51921 (48510) hydrogen bonds : bond 0.03774 ( 1631) hydrogen bonds : angle 4.70227 ( 4590) Misc. bond : bond 0.00013 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8833 (tmm) cc_final: 0.8216 (tmm) REVERT: B 534 PHE cc_start: 0.9073 (m-80) cc_final: 0.8699 (m-80) REVERT: C 522 MET cc_start: 0.8737 (tmm) cc_final: 0.8469 (tmm) REVERT: C 613 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8696 (mt) REVERT: C 682 MET cc_start: 0.4393 (mmm) cc_final: 0.4170 (mmt) REVERT: D 522 MET cc_start: 0.8110 (tmm) cc_final: 0.7639 (tmm) REVERT: D 600 CYS cc_start: 0.9097 (p) cc_final: 0.8694 (p) REVERT: E 522 MET cc_start: 0.8752 (tmm) cc_final: 0.8211 (tmm) REVERT: E 524 ASP cc_start: 0.8846 (m-30) cc_final: 0.8433 (t0) REVERT: E 680 MET cc_start: 0.5959 (tmm) cc_final: 0.5665 (tmm) REVERT: F 522 MET cc_start: 0.8435 (tmm) cc_final: 0.7610 (tmm) REVERT: F 534 PHE cc_start: 0.9215 (m-80) cc_final: 0.8941 (m-80) REVERT: F 677 MET cc_start: 0.2538 (OUTLIER) cc_final: 0.1924 (mtm) REVERT: G 408 MET cc_start: 0.4099 (OUTLIER) cc_final: 0.3762 (ptp) REVERT: I 425 MET cc_start: 0.9049 (tpp) cc_final: 0.8377 (tpp) REVERT: H 408 MET cc_start: 0.4584 (OUTLIER) cc_final: 0.4121 (ptp) REVERT: H 452 MET cc_start: 0.9052 (mmm) cc_final: 0.8794 (mtp) outliers start: 25 outliers final: 11 residues processed: 252 average time/residue: 0.1921 time to fit residues: 84.2340 Evaluate side-chains 250 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain D residue 584 GLN Chi-restraints excluded: chain D residue 684 HIS Chi-restraints excluded: chain F residue 677 MET Chi-restraints excluded: chain G residue 408 MET Chi-restraints excluded: chain G residue 526 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain K residue 526 VAL Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 563 MET Chi-restraints excluded: chain H residue 408 MET Chi-restraints excluded: chain H residue 526 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 21 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 303 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 4 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 616 ASN D 616 ASN E 684 HIS F 510 GLN F 684 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067661 restraints weight = 166066.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069113 restraints weight = 96526.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069898 restraints weight = 71053.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070493 restraints weight = 59854.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070609 restraints weight = 53790.526| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35892 Z= 0.120 Angle : 0.508 10.708 48510 Z= 0.262 Chirality : 0.043 0.165 5340 Planarity : 0.003 0.037 6294 Dihedral : 8.569 89.521 5346 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.68 % Allowed : 12.35 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4506 helix: 2.41 (0.13), residues: 1656 sheet: 0.88 (0.18), residues: 798 loop : -0.42 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 551 TYR 0.028 0.001 TYR B 590 PHE 0.009 0.001 PHE H 240 TRP 0.004 0.001 TRP L 276 HIS 0.017 0.001 HIS D 684 Details of bonding type rmsd covalent geometry : bond 0.00263 (35886) covalent geometry : angle 0.50817 (48510) hydrogen bonds : bond 0.03618 ( 1631) hydrogen bonds : angle 4.60806 ( 4590) Misc. bond : bond 0.00017 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8835 (tmm) cc_final: 0.8199 (tmm) REVERT: B 534 PHE cc_start: 0.9085 (m-80) cc_final: 0.8737 (m-80) REVERT: C 522 MET cc_start: 0.8743 (tmm) cc_final: 0.8456 (tmm) REVERT: C 557 ASP cc_start: 0.7792 (t0) cc_final: 0.7577 (t0) REVERT: C 597 TYR cc_start: 0.8406 (m-80) cc_final: 0.7937 (m-80) REVERT: C 613 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8744 (mt) REVERT: D 522 MET cc_start: 0.8055 (tmm) cc_final: 0.7550 (tmm) REVERT: D 533 GLN cc_start: 0.8912 (pm20) cc_final: 0.8313 (pm20) REVERT: D 600 CYS cc_start: 0.9095 (p) cc_final: 0.8721 (p) REVERT: E 522 MET cc_start: 0.8741 (tmm) cc_final: 0.8102 (tmm) REVERT: F 522 MET cc_start: 0.8460 (tmm) cc_final: 0.7597 (tmm) REVERT: F 534 PHE cc_start: 0.9229 (m-80) cc_final: 0.8933 (m-80) REVERT: G 408 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.3806 (ptp) REVERT: I 425 MET cc_start: 0.9025 (tpp) cc_final: 0.8383 (tpp) REVERT: H 213 MET cc_start: 0.8075 (mpp) cc_final: 0.7779 (mpp) REVERT: H 408 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.4339 (ptp) REVERT: H 452 MET cc_start: 0.9039 (mmm) cc_final: 0.8826 (mtp) outliers start: 25 outliers final: 13 residues processed: 252 average time/residue: 0.1908 time to fit residues: 84.1026 Evaluate side-chains 253 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain D residue 584 GLN Chi-restraints excluded: chain E residue 570 HIS Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 684 HIS Chi-restraints excluded: chain F residue 684 HIS Chi-restraints excluded: chain G residue 408 MET Chi-restraints excluded: chain G residue 526 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain K residue 526 VAL Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 563 MET Chi-restraints excluded: chain H residue 408 MET Chi-restraints excluded: chain H residue 526 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 145 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 390 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 378 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 312 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 616 ASN B 616 ASN D 616 ASN D 684 HIS G 389 GLN ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066743 restraints weight = 164951.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.068116 restraints weight = 97933.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068927 restraints weight = 72440.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069340 restraints weight = 61091.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.069470 restraints weight = 55782.022| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35892 Z= 0.185 Angle : 0.542 11.305 48510 Z= 0.280 Chirality : 0.043 0.171 5340 Planarity : 0.003 0.035 6294 Dihedral : 8.558 87.707 5346 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.76 % Allowed : 12.76 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4506 helix: 2.37 (0.13), residues: 1656 sheet: 0.83 (0.18), residues: 804 loop : -0.40 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 551 TYR 0.022 0.001 TYR C 590 PHE 0.010 0.001 PHE H 240 TRP 0.004 0.001 TRP L 276 HIS 0.018 0.001 HIS E 684 Details of bonding type rmsd covalent geometry : bond 0.00405 (35886) covalent geometry : angle 0.54188 (48510) hydrogen bonds : bond 0.03921 ( 1631) hydrogen bonds : angle 4.70639 ( 4590) Misc. bond : bond 0.00015 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8837 (tmm) cc_final: 0.8195 (tmm) REVERT: B 534 PHE cc_start: 0.9101 (m-80) cc_final: 0.8749 (m-80) REVERT: B 553 MET cc_start: 0.8920 (mtt) cc_final: 0.8658 (mtt) REVERT: B 584 GLN cc_start: 0.9106 (mp10) cc_final: 0.8731 (mp10) REVERT: C 522 MET cc_start: 0.8771 (tmm) cc_final: 0.8016 (tmm) REVERT: C 557 ASP cc_start: 0.7753 (t0) cc_final: 0.7539 (t70) REVERT: C 597 TYR cc_start: 0.8424 (m-80) cc_final: 0.7918 (m-80) REVERT: C 613 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8768 (mt) REVERT: D 522 MET cc_start: 0.8090 (tmm) cc_final: 0.7572 (tmm) REVERT: D 533 GLN cc_start: 0.8944 (pm20) cc_final: 0.8323 (pm20) REVERT: D 600 CYS cc_start: 0.9117 (p) cc_final: 0.8781 (p) REVERT: E 522 MET cc_start: 0.8724 (tmm) cc_final: 0.8099 (tmm) REVERT: E 680 MET cc_start: 0.5678 (tmm) cc_final: 0.5461 (tmm) REVERT: F 522 MET cc_start: 0.8488 (tmm) cc_final: 0.7651 (tmm) REVERT: G 408 MET cc_start: 0.4172 (OUTLIER) cc_final: 0.3810 (ptp) REVERT: G 452 MET cc_start: 0.9413 (mtp) cc_final: 0.9076 (mtp) REVERT: G 563 MET cc_start: 0.8030 (mmm) cc_final: 0.7767 (mmm) REVERT: I 408 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.4259 (ptp) REVERT: I 425 MET cc_start: 0.9054 (tpp) cc_final: 0.8399 (tpp) REVERT: H 213 MET cc_start: 0.8128 (mpp) cc_final: 0.7784 (mpp) REVERT: H 408 MET cc_start: 0.4620 (OUTLIER) cc_final: 0.4314 (ptp) outliers start: 28 outliers final: 10 residues processed: 257 average time/residue: 0.1943 time to fit residues: 86.5311 Evaluate side-chains 249 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain D residue 584 GLN Chi-restraints excluded: chain D residue 684 HIS Chi-restraints excluded: chain E residue 570 HIS Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain G residue 408 MET Chi-restraints excluded: chain G residue 526 VAL Chi-restraints excluded: chain I residue 408 MET Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain K residue 526 VAL Chi-restraints excluded: chain L residue 563 MET Chi-restraints excluded: chain H residue 408 MET Chi-restraints excluded: chain H residue 526 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 56 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 329 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 616 ASN B 570 HIS B 616 ASN B 684 HIS C 570 HIS D 570 HIS E 531 HIS E 684 HIS F 616 ASN F 684 HIS G 433 GLN I 402 GLN ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 402 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.083022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065600 restraints weight = 170389.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.066912 restraints weight = 99639.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067508 restraints weight = 73191.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068089 restraints weight = 63438.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068291 restraints weight = 56534.819| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 35892 Z= 0.349 Angle : 0.680 11.400 48510 Z= 0.361 Chirality : 0.046 0.195 5340 Planarity : 0.004 0.035 6294 Dihedral : 8.868 89.535 5346 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.71 % Allowed : 13.27 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4506 helix: 1.81 (0.13), residues: 1656 sheet: 0.61 (0.18), residues: 744 loop : -0.55 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 551 TYR 0.034 0.002 TYR B 590 PHE 0.014 0.002 PHE J 191 TRP 0.005 0.001 TRP J 527 HIS 0.037 0.002 HIS D 684 Details of bonding type rmsd covalent geometry : bond 0.00747 (35886) covalent geometry : angle 0.68040 (48510) hydrogen bonds : bond 0.05350 ( 1631) hydrogen bonds : angle 5.32307 ( 4590) Misc. bond : bond 0.00044 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8765 (tmm) cc_final: 0.8246 (tmm) REVERT: B 534 PHE cc_start: 0.9119 (m-80) cc_final: 0.8752 (m-80) REVERT: B 584 GLN cc_start: 0.9083 (mp10) cc_final: 0.8709 (mp10) REVERT: C 522 MET cc_start: 0.8739 (tmm) cc_final: 0.8012 (tmm) REVERT: C 524 ASP cc_start: 0.8751 (m-30) cc_final: 0.8491 (t0) REVERT: C 682 MET cc_start: 0.5096 (mmm) cc_final: 0.4485 (tpt) REVERT: D 522 MET cc_start: 0.8166 (tmm) cc_final: 0.7894 (tmm) REVERT: D 533 GLN cc_start: 0.9048 (pm20) cc_final: 0.8392 (pm20) REVERT: D 600 CYS cc_start: 0.9007 (p) cc_final: 0.8699 (p) REVERT: E 522 MET cc_start: 0.8705 (tmm) cc_final: 0.8306 (tmm) REVERT: E 524 ASP cc_start: 0.8826 (m-30) cc_final: 0.8510 (t0) REVERT: F 522 MET cc_start: 0.8487 (tmm) cc_final: 0.7681 (tmm) REVERT: F 682 MET cc_start: 0.5787 (tpt) cc_final: 0.5411 (tpp) REVERT: G 408 MET cc_start: 0.4335 (OUTLIER) cc_final: 0.3948 (ptp) REVERT: I 408 MET cc_start: 0.4703 (OUTLIER) cc_final: 0.4429 (ptp) REVERT: H 213 MET cc_start: 0.8138 (mpp) cc_final: 0.7661 (mpp) outliers start: 26 outliers final: 6 residues processed: 263 average time/residue: 0.1935 time to fit residues: 88.7255 Evaluate side-chains 255 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 247 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain D residue 584 GLN Chi-restraints excluded: chain E residue 570 HIS Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 684 HIS Chi-restraints excluded: chain G residue 408 MET Chi-restraints excluded: chain I residue 408 MET Chi-restraints excluded: chain L residue 563 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 76 optimal weight: 0.1980 chunk 446 optimal weight: 2.9990 chunk 391 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 328 optimal weight: 0.9990 chunk 286 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS B 616 ASN C 616 ASN D 684 HIS F 684 HIS I 402 GLN J 372 ASN J 402 GLN K 372 ASN K 402 GLN L 372 ASN L 402 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.085017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067391 restraints weight = 165052.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068750 restraints weight = 95556.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069611 restraints weight = 70059.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069929 restraints weight = 58481.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070352 restraints weight = 53927.483| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35892 Z= 0.109 Angle : 0.560 13.175 48510 Z= 0.287 Chirality : 0.044 0.159 5340 Planarity : 0.003 0.034 6294 Dihedral : 8.602 87.245 5346 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.60 % Allowed : 13.87 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.13), residues: 4506 helix: 2.22 (0.13), residues: 1662 sheet: 0.80 (0.19), residues: 690 loop : -0.47 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 551 TYR 0.022 0.001 TYR B 590 PHE 0.009 0.001 PHE G 561 TRP 0.005 0.001 TRP L 465 HIS 0.014 0.001 HIS F 684 Details of bonding type rmsd covalent geometry : bond 0.00229 (35886) covalent geometry : angle 0.55971 (48510) hydrogen bonds : bond 0.03894 ( 1631) hydrogen bonds : angle 4.60980 ( 4590) Misc. bond : bond 0.00017 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8785 (tmm) cc_final: 0.8281 (tmm) REVERT: B 534 PHE cc_start: 0.9027 (m-80) cc_final: 0.8678 (m-80) REVERT: B 584 GLN cc_start: 0.9133 (mp10) cc_final: 0.8756 (mp10) REVERT: C 522 MET cc_start: 0.8754 (tmm) cc_final: 0.8261 (tmm) REVERT: C 682 MET cc_start: 0.4814 (mmm) cc_final: 0.4103 (tpt) REVERT: D 522 MET cc_start: 0.8207 (tmm) cc_final: 0.7670 (tmm) REVERT: D 600 CYS cc_start: 0.9041 (p) cc_final: 0.8709 (p) REVERT: E 522 MET cc_start: 0.8679 (tmm) cc_final: 0.8325 (tmm) REVERT: F 522 MET cc_start: 0.8475 (tmm) cc_final: 0.7647 (tmm) REVERT: F 682 MET cc_start: 0.5449 (tpt) cc_final: 0.5025 (tpp) REVERT: J 213 MET cc_start: 0.7873 (mpp) cc_final: 0.7515 (mpp) REVERT: K 213 MET cc_start: 0.7885 (mpp) cc_final: 0.7541 (mpp) REVERT: L 201 MET cc_start: 0.8684 (mtt) cc_final: 0.8422 (mtt) REVERT: H 213 MET cc_start: 0.7950 (mpp) cc_final: 0.7672 (mpp) REVERT: H 408 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.4149 (ptp) outliers start: 22 outliers final: 12 residues processed: 250 average time/residue: 0.1941 time to fit residues: 84.4969 Evaluate side-chains 253 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain D residue 584 GLN Chi-restraints excluded: chain D residue 684 HIS Chi-restraints excluded: chain E residue 570 HIS Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 684 HIS Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain K residue 526 VAL Chi-restraints excluded: chain L residue 563 MET Chi-restraints excluded: chain H residue 408 MET Chi-restraints excluded: chain H residue 526 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 261 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 214 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 320 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 127 optimal weight: 0.0060 chunk 187 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 overall best weight: 3.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 616 ASN B 616 ASN C 510 GLN C 570 HIS C 616 ASN D 684 HIS F 684 HIS J 372 ASN K 372 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.084489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066892 restraints weight = 168406.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068249 restraints weight = 97004.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069001 restraints weight = 70959.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069534 restraints weight = 59997.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.069795 restraints weight = 53916.844| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35892 Z= 0.168 Angle : 0.551 12.936 48510 Z= 0.286 Chirality : 0.043 0.170 5340 Planarity : 0.003 0.039 6294 Dihedral : 8.515 85.455 5346 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.38 % Allowed : 13.95 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4506 helix: 2.21 (0.13), residues: 1662 sheet: 0.86 (0.18), residues: 744 loop : -0.48 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 551 TYR 0.024 0.001 TYR B 590 PHE 0.009 0.001 PHE H 240 TRP 0.005 0.001 TRP H 276 HIS 0.012 0.001 HIS F 684 Details of bonding type rmsd covalent geometry : bond 0.00369 (35886) covalent geometry : angle 0.55119 (48510) hydrogen bonds : bond 0.03949 ( 1631) hydrogen bonds : angle 4.68623 ( 4590) Misc. bond : bond 0.00016 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8796 (tmm) cc_final: 0.8296 (tmm) REVERT: A 533 GLN cc_start: 0.9058 (pm20) cc_final: 0.8671 (pm20) REVERT: B 534 PHE cc_start: 0.9057 (m-80) cc_final: 0.8685 (m-80) REVERT: B 584 GLN cc_start: 0.9130 (mp10) cc_final: 0.8749 (mp10) REVERT: C 522 MET cc_start: 0.8727 (tmm) cc_final: 0.8098 (tmm) REVERT: C 682 MET cc_start: 0.4836 (mmm) cc_final: 0.4139 (tpt) REVERT: D 522 MET cc_start: 0.8179 (tmm) cc_final: 0.7896 (tmm) REVERT: D 533 GLN cc_start: 0.8957 (pm20) cc_final: 0.8338 (pm20) REVERT: D 600 CYS cc_start: 0.9041 (p) cc_final: 0.8730 (p) REVERT: E 522 MET cc_start: 0.8695 (tmm) cc_final: 0.8310 (tmm) REVERT: F 522 MET cc_start: 0.8519 (tmm) cc_final: 0.7671 (tmm) REVERT: F 682 MET cc_start: 0.5347 (tpt) cc_final: 0.4897 (tpp) REVERT: H 213 MET cc_start: 0.8088 (mpp) cc_final: 0.7764 (mpp) REVERT: H 408 MET cc_start: 0.4583 (OUTLIER) cc_final: 0.4156 (ptp) outliers start: 14 outliers final: 12 residues processed: 247 average time/residue: 0.1946 time to fit residues: 83.6484 Evaluate side-chains 252 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain D residue 584 GLN Chi-restraints excluded: chain D residue 684 HIS Chi-restraints excluded: chain E residue 570 HIS Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 684 HIS Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain K residue 526 VAL Chi-restraints excluded: chain L residue 563 MET Chi-restraints excluded: chain H residue 408 MET Chi-restraints excluded: chain H residue 526 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 298 optimal weight: 0.9990 chunk 402 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 356 optimal weight: 0.0770 chunk 389 optimal weight: 0.9980 chunk 369 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 570 HIS C 616 ASN F 684 HIS J 372 ASN K 372 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.085430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067786 restraints weight = 164007.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069171 restraints weight = 96019.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070015 restraints weight = 71024.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070330 restraints weight = 59464.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.070696 restraints weight = 54903.868| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35892 Z= 0.107 Angle : 0.538 12.878 48510 Z= 0.276 Chirality : 0.043 0.160 5340 Planarity : 0.003 0.034 6294 Dihedral : 8.415 84.221 5346 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.43 % Allowed : 14.09 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.13), residues: 4506 helix: 2.26 (0.13), residues: 1668 sheet: 0.92 (0.19), residues: 690 loop : -0.45 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 551 TYR 0.022 0.001 TYR B 590 PHE 0.008 0.001 PHE H 240 TRP 0.004 0.001 TRP H 276 HIS 0.010 0.001 HIS F 684 Details of bonding type rmsd covalent geometry : bond 0.00233 (35886) covalent geometry : angle 0.53789 (48510) hydrogen bonds : bond 0.03634 ( 1631) hydrogen bonds : angle 4.52039 ( 4590) Misc. bond : bond 0.00020 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4885.60 seconds wall clock time: 86 minutes 40.70 seconds (5200.70 seconds total)