Starting phenix.real_space_refine on Fri Feb 23 07:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd4_31534/02_2024/7fd4_31534_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 136 5.16 5 B 6 2.79 5 C 23460 2.51 5 N 6514 2.21 5 O 7050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 432": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 385": "NH1" <-> "NH2" Residue "E ARG 432": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 250": "NH1" <-> "NH2" Residue "F ARG 432": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 709": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37182 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "S" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.65, per 1000 atoms: 0.53 Number of scatterers: 37182 At special positions: 0 Unit cell: (182.86, 189.42, 201.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 16 15.00 O 7050 8.00 N 6514 7.00 C 23460 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.68 Conformation dependent library (CDL) restraints added in 6.8 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 35 sheets defined 40.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.51 Creating SS restraints... Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 118 through 138 Processing helix chain 'B' and resid 149 through 154 removed outlier: 6.177A pdb=" N GLY B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 186 through 237 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.943A pdb=" N LYS B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.505A pdb=" N GLN B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 362 through 371 removed outlier: 4.132A pdb=" N ARG B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 369 " --> pdb=" O ARG B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.561A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.602A pdb=" N SER B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.518A pdb=" N GLU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.532A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 741 through 745' Processing helix chain 'B' and resid 748 through 751 No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'C' and resid 28 through 38 removed outlier: 4.701A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 136 through 142 removed outlier: 5.493A pdb=" N SER C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 237 removed outlier: 3.585A pdb=" N ARG C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 260 through 275 removed outlier: 4.035A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.754A pdb=" N TYR C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.777A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU C 317 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 362 through 371 removed outlier: 4.254A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 435 through 438 No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.963A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 513 Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 541 through 560 removed outlier: 3.603A pdb=" N ARG C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.670A pdb=" N ILE C 574 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Proline residue: C 575 - end of helix removed outlier: 3.999A pdb=" N LEU C 578 " --> pdb=" O PRO C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 571 through 578' Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.522A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 680 through 691 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 745 removed outlier: 3.868A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 741 through 745' Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.570A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 39 removed outlier: 3.580A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 removed outlier: 3.526A pdb=" N ASN D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 239 Processing helix chain 'D' and resid 245 through 255 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.034A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.052A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 435 through 441 removed outlier: 4.510A pdb=" N GLU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 4.353A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.606A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 560 Processing helix chain 'D' and resid 571 through 577 removed outlier: 3.555A pdb=" N ILE D 574 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Proline residue: D 575 - end of helix No H-bonds generated for 'chain 'D' and resid 571 through 577' Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.575A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 728 Processing helix chain 'D' and resid 737 through 739 No H-bonds generated for 'chain 'D' and resid 737 through 739' Processing helix chain 'D' and resid 741 through 744 removed outlier: 3.842A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.970A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'E' and resid 31 through 38 removed outlier: 3.568A pdb=" N MET E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 141 removed outlier: 4.442A pdb=" N LYS E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 186 through 237 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 260 through 270 Processing helix chain 'E' and resid 283 through 295 Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.734A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 removed outlier: 3.570A pdb=" N TYR E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 437 through 443 removed outlier: 3.512A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 450 removed outlier: 3.755A pdb=" N THR E 450 " --> pdb=" O GLN E 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 447 through 450' Processing helix chain 'E' and resid 479 through 484 removed outlier: 4.052A pdb=" N ARG E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 560 Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 651 removed outlier: 3.556A pdb=" N HIS E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 648 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP E 650 " --> pdb=" O ALA E 646 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 737 through 745 removed outlier: 4.651A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 762 through 769 removed outlier: 3.504A pdb=" N TYR E 768 " --> pdb=" O GLU E 764 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 removed outlier: 4.162A pdb=" N ARG F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 138 removed outlier: 3.842A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN F 138 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 150 No H-bonds generated for 'chain 'F' and resid 147 through 150' Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.610A pdb=" N HIS F 168 " --> pdb=" O THR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 185 through 237 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 260 through 268 removed outlier: 4.274A pdb=" N LYS F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 308 through 315 Processing helix chain 'F' and resid 323 through 338 Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 387 through 389 No H-bonds generated for 'chain 'F' and resid 387 through 389' Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 424 through 426 No H-bonds generated for 'chain 'F' and resid 424 through 426' Processing helix chain 'F' and resid 436 through 443 Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 495 through 514 removed outlier: 3.561A pdb=" N GLN F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Proline residue: F 508 - end of helix removed outlier: 3.897A pdb=" N SER F 514 " --> pdb=" O GLN F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 534 Processing helix chain 'F' and resid 541 through 558 removed outlier: 3.704A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 578 Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 726 Processing helix chain 'F' and resid 737 through 744 removed outlier: 4.987A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 No H-bonds generated for 'chain 'F' and resid 748 through 751' Processing helix chain 'F' and resid 762 through 769 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 118 through 139 removed outlier: 4.959A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 236 Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.575A pdb=" N GLU A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.545A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.780A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.212A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.974A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.869A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 495 through 513 removed outlier: 4.977A pdb=" N TRP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.562A pdb=" N LEU A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 737 through 745 removed outlier: 3.502A pdb=" N GLU A 740 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 744 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 No H-bonds generated for 'chain 'A' and resid 748 through 751' Processing helix chain 'A' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'B' and resid 20 through 25 Processing sheet with id= B, first strand: chain 'B' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.851A pdb=" N PHE B 467 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLY B 355 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 471 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.247A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 596 through 602 removed outlier: 5.887A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL B 667 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR B 626 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 733 through 736 Processing sheet with id= G, first strand: chain 'C' and resid 74 through 76 removed outlier: 4.176A pdb=" N MET C 75 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 83 " --> pdb=" O MET C 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 486 through 489 removed outlier: 6.710A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 596 through 603 removed outlier: 5.987A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL C 667 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR C 626 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.686A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 65 through 71 removed outlier: 4.081A pdb=" N ALA C 90 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 43 through 46 Processing sheet with id= M, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.865A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 486 through 490 removed outlier: 6.901A pdb=" N PHE D 467 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU D 353 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 469 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY D 355 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA D 471 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 470 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 596 through 603 removed outlier: 6.264A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL D 667 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR D 626 " --> pdb=" O VAL D 667 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.249A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 69 through 76 removed outlier: 4.388A pdb=" N VAL D 70 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 87 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA D 74 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN D 83 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 43 through 45 removed outlier: 3.616A pdb=" N ALA E 69 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 486 through 489 removed outlier: 7.462A pdb=" N PHE E 467 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEU E 353 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 469 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.044A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 596 through 600 removed outlier: 3.550A pdb=" N VAL E 667 " --> pdb=" O THR E 626 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.563A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 21 through 25 removed outlier: 4.268A pdb=" N VAL F 25 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.709A pdb=" N VAL F 67 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 485 through 490 removed outlier: 5.692A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE F 490 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL F 354 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU F 351 " --> pdb=" O PHE F 467 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.414A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 596 through 603 Processing sheet with id= AB, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.378A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.511A pdb=" N LEU A 3 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 104 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 98 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 96 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 7 through 10 removed outlier: 8.765A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 10 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL A 47 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.684A pdb=" N GLN A 73 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU A 87 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 71 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 485 through 490 removed outlier: 6.170A pdb=" N ILE A 350 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE A 488 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 490 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 354 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 351 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 355 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 375 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 420 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.299A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'A' and resid 596 through 603 Processing sheet with id= AI, first strand: chain 'A' and resid 733 through 736 1378 hydrogen bonds defined for protein. 4059 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: 12.82 Time building geometry restraints manager: 15.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 7397 1.32 - 1.48: 13750 1.48 - 1.64: 16456 1.64 - 1.79: 185 1.79 - 1.95: 83 Bond restraints: 37871 Sorted by residual: bond pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.21e-02 6.83e+03 7.76e+01 bond pdb=" C18 4KZ F 802 " pdb=" N20 4KZ F 802 " ideal model delta sigma weight residual 1.457 1.292 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C18 4KZ E 802 " pdb=" N20 4KZ E 802 " ideal model delta sigma weight residual 1.457 1.302 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" C18 4KZ C 802 " pdb=" N20 4KZ C 802 " ideal model delta sigma weight residual 1.457 1.308 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C7 4KZ C 802 " pdb=" N9 4KZ C 802 " ideal model delta sigma weight residual 1.455 1.306 0.149 2.00e-02 2.50e+03 5.53e+01 ... (remaining 37866 not shown) Histogram of bond angle deviations from ideal: 85.16 - 98.94: 22 98.94 - 112.72: 20963 112.72 - 126.50: 29782 126.50 - 140.28: 602 140.28 - 154.06: 2 Bond angle restraints: 51371 Sorted by residual: angle pdb=" O ALA D 679 " pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 122.42 85.16 37.26 1.61e+00 3.86e-01 5.36e+02 angle pdb=" CA ALA D 679 " pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 118.27 154.06 -35.79 1.59e+00 3.96e-01 5.07e+02 angle pdb=" C ALA D 679 " pdb=" N GLY D 680 " pdb=" CA GLY D 680 " ideal model delta sigma weight residual 120.00 143.91 -23.91 1.10e+00 8.26e-01 4.73e+02 angle pdb=" O ALA A 679 " pdb=" C ALA A 679 " pdb=" N GLY A 680 " ideal model delta sigma weight residual 122.20 102.98 19.22 1.28e+00 6.10e-01 2.26e+02 angle pdb=" O ALA C 679 " pdb=" C ALA C 679 " pdb=" N GLY C 680 " ideal model delta sigma weight residual 122.19 103.48 18.71 1.29e+00 6.01e-01 2.10e+02 ... (remaining 51366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 23025 32.82 - 65.65: 249 65.65 - 98.47: 44 98.47 - 131.30: 7 131.30 - 164.12: 2 Dihedral angle restraints: 23327 sinusoidal: 9768 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -108.81 -71.19 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ASP B 51 " pdb=" C ASP B 51 " pdb=" N PRO B 52 " pdb=" CA PRO B 52 " ideal model delta harmonic sigma weight residual -180.00 -108.94 -71.06 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -112.95 -67.05 0 5.00e+00 4.00e-02 1.80e+02 ... (remaining 23324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5529 0.126 - 0.251: 300 0.251 - 0.377: 12 0.377 - 0.503: 2 0.503 - 0.629: 1 Chirality restraints: 5844 Sorted by residual: chirality pdb=" CA ASP E 434 " pdb=" N ASP E 434 " pdb=" C ASP E 434 " pdb=" CB ASP E 434 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.88e+00 chirality pdb=" CA LEU C 243 " pdb=" N LEU C 243 " pdb=" C LEU C 243 " pdb=" CB LEU C 243 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA LEU F 246 " pdb=" N LEU F 246 " pdb=" C LEU F 246 " pdb=" CB LEU F 246 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 5841 not shown) Planarity restraints: 6657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 4KZ B 802 " -0.206 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C18 4KZ B 802 " 0.138 2.00e-02 2.50e+03 pdb=" C21 4KZ B 802 " -0.263 2.00e-02 2.50e+03 pdb=" N20 4KZ B 802 " 0.340 2.00e-02 2.50e+03 pdb=" O19 4KZ B 802 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ F 802 " 0.200 2.00e-02 2.50e+03 2.15e-01 5.77e+02 pdb=" C18 4KZ F 802 " -0.127 2.00e-02 2.50e+03 pdb=" C21 4KZ F 802 " 0.257 2.00e-02 2.50e+03 pdb=" N20 4KZ F 802 " -0.330 2.00e-02 2.50e+03 pdb=" O19 4KZ F 802 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ E 802 " -0.155 2.00e-02 2.50e+03 1.66e-01 3.43e+02 pdb=" C18 4KZ E 802 " 0.102 2.00e-02 2.50e+03 pdb=" C21 4KZ E 802 " -0.196 2.00e-02 2.50e+03 pdb=" N20 4KZ E 802 " 0.254 2.00e-02 2.50e+03 pdb=" O19 4KZ E 802 " -0.004 2.00e-02 2.50e+03 ... (remaining 6654 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4633 2.75 - 3.29: 33672 3.29 - 3.82: 58844 3.82 - 4.36: 69716 4.36 - 4.90: 119886 Nonbonded interactions: 286751 Sorted by model distance: nonbonded pdb=" O GLY F 676 " pdb=" CA PRO F 677 " model vdw 2.212 2.776 nonbonded pdb=" O ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.229 2.440 nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 801 " model vdw 2.242 2.440 nonbonded pdb=" OE1 GLU D 36 " pdb=" OH TYR D 102 " model vdw 2.246 2.440 nonbonded pdb=" O1B AGS C 801 " pdb=" O2G AGS C 801 " model vdw 2.246 2.440 ... (remaining 286746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 780 or resid 802)) selection = (chain 'B' and (resid 2 through 780 or resid 802)) selection = (chain 'C' and (resid 2 through 780 or resid 802)) selection = (chain 'D' and (resid 2 through 780 or resid 802)) selection = (chain 'E' and (resid 2 through 780 or resid 802)) selection = (chain 'F' and (resid 2 through 780 or resid 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 10.440 Check model and map are aligned: 0.600 Set scattering table: 0.310 Process input model: 95.230 Find NCS groups from input model: 3.050 Set up NCS constraints: 0.250 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.165 37871 Z= 0.701 Angle : 1.186 37.259 51371 Z= 0.663 Chirality : 0.065 0.629 5844 Planarity : 0.010 0.222 6657 Dihedral : 11.322 164.121 14595 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 0.41 % Allowed : 2.72 % Favored : 96.87 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 3.26 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.10), residues: 4662 helix: -2.35 (0.09), residues: 2009 sheet: -1.25 (0.19), residues: 639 loop : -2.91 (0.11), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP F 171 HIS 0.021 0.003 HIS C 454 PHE 0.030 0.003 PHE C 467 TYR 0.039 0.003 TYR B 97 ARG 0.019 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 381 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 748 LYS cc_start: 0.8988 (mmpt) cc_final: 0.8746 (mppt) REVERT: C 38 MET cc_start: 0.0145 (mmt) cc_final: -0.0237 (mmt) REVERT: C 308 ILE cc_start: 0.8307 (pt) cc_final: 0.8010 (mt) REVERT: C 385 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7646 (ttp-170) REVERT: D 401 MET cc_start: 0.8720 (ptt) cc_final: 0.8461 (ptp) REVERT: E 38 MET cc_start: 0.2035 (mtt) cc_final: 0.1261 (tmm) REVERT: E 75 MET cc_start: 0.1492 (ttp) cc_final: 0.1102 (ttp) REVERT: E 252 LYS cc_start: 0.6662 (ptmt) cc_final: 0.6320 (tttp) REVERT: F 38 MET cc_start: 0.0830 (mtp) cc_final: 0.0593 (ptp) REVERT: F 347 LYS cc_start: 0.7599 (tptt) cc_final: 0.7265 (tmtt) REVERT: F 372 MET cc_start: 0.8660 (mtm) cc_final: 0.8150 (mtm) REVERT: F 390 ILE cc_start: 0.7379 (mm) cc_final: 0.7071 (mp) REVERT: F 393 HIS cc_start: 0.6732 (m-70) cc_final: 0.6412 (m170) REVERT: F 442 VAL cc_start: 0.8187 (p) cc_final: 0.7958 (m) REVERT: F 481 LEU cc_start: 0.8030 (mp) cc_final: 0.7747 (mt) REVERT: F 485 MET cc_start: 0.7022 (pmt) cc_final: 0.5861 (mmm) REVERT: A 323 LYS cc_start: 0.8278 (mmpt) cc_final: 0.7986 (mtpp) REVERT: A 412 VAL cc_start: 0.8006 (t) cc_final: 0.7787 (m) REVERT: A 660 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8521 (mmmt) outliers start: 16 outliers final: 5 residues processed: 395 average time/residue: 2.0486 time to fit residues: 932.6514 Evaluate side-chains 234 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 483 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 237 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 363 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 270 optimal weight: 9.9990 chunk 421 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS B 346 ASN B 495 ASN B 666 HIS C 83 GLN C 138 ASN C 393 HIS C 454 HIS C 664 HIS C 739 ASN C 742 GLN D 12 ASN D 139 HIS D 393 HIS D 407 HIS D 510 GLN D 739 ASN E 138 ASN E 216 GLN E 220 ASN E 319 HIS E 340 GLN E 510 GLN E 598 GLN E 649 GLN F 49 GLN F 168 HIS F 177 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 HIS A 234 GLN A 319 HIS ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 739 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37871 Z= 0.171 Angle : 0.626 11.686 51371 Z= 0.316 Chirality : 0.044 0.198 5844 Planarity : 0.006 0.077 6657 Dihedral : 9.506 161.776 5327 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 1.63 % Allowed : 6.87 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 4662 helix: -0.47 (0.11), residues: 2024 sheet: -0.93 (0.19), residues: 656 loop : -2.42 (0.12), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 171 HIS 0.004 0.001 HIS F 664 PHE 0.015 0.001 PHE C 467 TYR 0.018 0.001 TYR E 289 ARG 0.007 0.001 ARG E 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 262 time to evaluate : 4.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1109 (OUTLIER) cc_final: -0.0083 (pmm) REVERT: B 713 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: B 748 LYS cc_start: 0.9000 (mmpt) cc_final: 0.8708 (mppt) REVERT: C 38 MET cc_start: 0.0165 (mmt) cc_final: -0.0153 (mmt) REVERT: C 385 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7185 (ttt90) REVERT: C 398 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8110 (mm) REVERT: C 479 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7891 (mmp-170) REVERT: C 511 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (p) REVERT: D 401 MET cc_start: 0.8650 (ptt) cc_final: 0.8422 (ptp) REVERT: E 38 MET cc_start: 0.2112 (mtt) cc_final: 0.1242 (tmm) REVERT: E 75 MET cc_start: 0.1624 (ttp) cc_final: 0.1203 (ttp) REVERT: E 252 LYS cc_start: 0.6590 (ptmt) cc_final: 0.6119 (tttp) REVERT: F 276 MET cc_start: 0.5211 (mtp) cc_final: 0.4462 (mpp) REVERT: F 313 GLN cc_start: 0.7419 (mm110) cc_final: 0.7219 (mm110) REVERT: F 347 LYS cc_start: 0.7736 (tptt) cc_final: 0.7398 (tmtt) REVERT: F 372 MET cc_start: 0.8618 (mtm) cc_final: 0.8046 (mtm) REVERT: F 393 HIS cc_start: 0.6707 (m-70) cc_final: 0.6404 (m170) REVERT: F 483 ASP cc_start: 0.7421 (p0) cc_final: 0.7000 (p0) REVERT: F 485 MET cc_start: 0.7063 (pmt) cc_final: 0.5920 (mmm) REVERT: F 546 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 38 MET cc_start: 0.1930 (tpt) cc_final: 0.0519 (ptt) REVERT: A 660 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8517 (mmmt) outliers start: 64 outliers final: 15 residues processed: 304 average time/residue: 1.6970 time to fit residues: 613.2491 Evaluate side-chains 232 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 727 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 422 optimal weight: 0.3980 chunk 456 optimal weight: 6.9990 chunk 375 optimal weight: 10.0000 chunk 418 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 338 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS C 83 GLN C 475 GLN D 346 ASN D 647 HIS E 647 HIS F 337 GLN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37871 Z= 0.360 Angle : 0.686 11.327 51371 Z= 0.340 Chirality : 0.047 0.265 5844 Planarity : 0.006 0.073 6657 Dihedral : 8.981 160.582 5325 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.27 % Rotamer: Outliers : 2.24 % Allowed : 7.94 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.54 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 4662 helix: 0.25 (0.12), residues: 2052 sheet: -0.69 (0.20), residues: 646 loop : -2.18 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 602 HIS 0.009 0.001 HIS B 454 PHE 0.029 0.002 PHE B 466 TYR 0.025 0.002 TYR A 332 ARG 0.006 0.001 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 219 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1330 (mmt) cc_final: 0.0172 (pmm) REVERT: B 748 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8730 (mppt) REVERT: C 38 MET cc_start: -0.0008 (mmt) cc_final: -0.0290 (mmt) REVERT: C 337 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: C 385 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7556 (ttp-170) REVERT: C 511 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 586 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7926 (p0) REVERT: D 422 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8585 (t0) REVERT: D 556 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7299 (tttp) REVERT: E 38 MET cc_start: 0.2235 (mtt) cc_final: 0.1109 (tmm) REVERT: E 75 MET cc_start: 0.1696 (ttp) cc_final: 0.1235 (ttp) REVERT: E 252 LYS cc_start: 0.6520 (ptmt) cc_final: 0.6126 (tttp) REVERT: F 276 MET cc_start: 0.5177 (mtp) cc_final: 0.4306 (mpp) REVERT: F 313 GLN cc_start: 0.7425 (mm110) cc_final: 0.7215 (mm110) REVERT: F 347 LYS cc_start: 0.7693 (tptt) cc_final: 0.7351 (tmtt) REVERT: F 372 MET cc_start: 0.8614 (mtm) cc_final: 0.8096 (mtm) REVERT: F 393 HIS cc_start: 0.6692 (m-70) cc_final: 0.6400 (m170) REVERT: F 483 ASP cc_start: 0.7400 (p0) cc_final: 0.7014 (p0) REVERT: F 485 MET cc_start: 0.7014 (pmt) cc_final: 0.6005 (mmm) REVERT: F 546 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 38 MET cc_start: 0.2059 (tpt) cc_final: 0.0542 (ptt) REVERT: A 484 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7376 (mtm-85) REVERT: A 591 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 660 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8546 (mmmt) outliers start: 88 outliers final: 33 residues processed: 284 average time/residue: 1.6797 time to fit residues: 567.5920 Evaluate side-chains 253 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 212 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 466 PHE Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 3.9990 chunk 317 optimal weight: 0.0470 chunk 219 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 423 optimal weight: 8.9990 chunk 448 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 401 optimal weight: 40.0000 chunk 120 optimal weight: 0.8980 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN F 68 GLN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37871 Z= 0.232 Angle : 0.596 14.388 51371 Z= 0.294 Chirality : 0.044 0.208 5844 Planarity : 0.005 0.074 6657 Dihedral : 8.466 161.375 5323 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 2.29 % Allowed : 8.98 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.54 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4662 helix: 0.79 (0.12), residues: 2041 sheet: -0.42 (0.20), residues: 647 loop : -2.01 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 171 HIS 0.005 0.001 HIS B 454 PHE 0.016 0.001 PHE B 466 TYR 0.017 0.001 TYR A 332 ARG 0.005 0.000 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 220 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1278 (mmt) cc_final: 0.0112 (pmm) REVERT: B 251 LYS cc_start: 0.9142 (ttpt) cc_final: 0.8907 (tttm) REVERT: B 479 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7484 (mpt180) REVERT: B 713 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8593 (mtm) REVERT: B 748 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8732 (mppt) REVERT: C 38 MET cc_start: 0.0010 (mmt) cc_final: -0.0253 (mmt) REVERT: C 385 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7137 (ttt90) REVERT: C 398 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7986 (mm) REVERT: C 479 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7214 (mpt180) REVERT: C 586 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7872 (p0) REVERT: C 683 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: D 422 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8595 (t0) REVERT: D 556 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7226 (tttp) REVERT: E 38 MET cc_start: 0.2498 (mtt) cc_final: 0.1259 (tmm) REVERT: E 75 MET cc_start: 0.1676 (ttp) cc_final: 0.1228 (ttp) REVERT: E 243 LEU cc_start: 0.3841 (OUTLIER) cc_final: 0.3637 (mt) REVERT: E 252 LYS cc_start: 0.6445 (ptmt) cc_final: 0.6060 (tttp) REVERT: F 276 MET cc_start: 0.5035 (mtp) cc_final: 0.4337 (mpp) REVERT: F 347 LYS cc_start: 0.7683 (tptt) cc_final: 0.7331 (tmtt) REVERT: F 372 MET cc_start: 0.8566 (mtm) cc_final: 0.8095 (mtm) REVERT: F 393 HIS cc_start: 0.6621 (m-70) cc_final: 0.6346 (m170) REVERT: F 435 PRO cc_start: 0.5823 (Cg_endo) cc_final: 0.5323 (Cg_exo) REVERT: F 483 ASP cc_start: 0.7415 (p0) cc_final: 0.7022 (p0) REVERT: F 485 MET cc_start: 0.7097 (pmt) cc_final: 0.6067 (mmm) REVERT: F 494 THR cc_start: 0.7701 (m) cc_final: 0.7465 (p) REVERT: F 546 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: A 38 MET cc_start: 0.2022 (tpt) cc_final: 0.0663 (ptt) REVERT: A 75 MET cc_start: -0.1691 (ttt) cc_final: -0.2138 (ttt) REVERT: A 247 GLU cc_start: 0.7544 (mp0) cc_final: 0.7283 (mp0) REVERT: A 308 ILE cc_start: 0.8373 (pt) cc_final: 0.8082 (mt) REVERT: A 484 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: A 591 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: A 660 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8490 (mmmt) outliers start: 90 outliers final: 35 residues processed: 284 average time/residue: 1.6601 time to fit residues: 562.8144 Evaluate side-chains 255 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 208 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 0.4980 chunk 254 optimal weight: 7.9990 chunk 6 optimal weight: 50.0000 chunk 333 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 310 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 229 optimal weight: 5.9990 chunk 402 optimal weight: 50.0000 chunk 113 optimal weight: 3.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 GLN C 309 ASN D 346 ASN D 495 ASN E 495 ASN E 727 GLN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 37871 Z= 0.462 Angle : 0.710 14.937 51371 Z= 0.350 Chirality : 0.049 0.204 5844 Planarity : 0.006 0.076 6657 Dihedral : 8.470 161.002 5323 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 2.24 % Allowed : 9.77 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4662 helix: 0.76 (0.12), residues: 2059 sheet: -0.30 (0.20), residues: 635 loop : -1.92 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 298 HIS 0.011 0.002 HIS B 454 PHE 0.028 0.002 PHE B 466 TYR 0.028 0.002 TYR F 577 ARG 0.011 0.001 ARG E 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 206 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1534 (mmt) cc_final: 0.0404 (pmm) REVERT: B 748 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8726 (mppt) REVERT: C 38 MET cc_start: 0.0086 (mmt) cc_final: -0.0296 (mmt) REVERT: C 359 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7319 (m) REVERT: C 385 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7764 (ttp-170) REVERT: C 586 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7873 (p0) REVERT: C 683 MET cc_start: 0.8714 (mtt) cc_final: 0.8042 (mtt) REVERT: D 405 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8476 (mm) REVERT: D 556 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7248 (tttp) REVERT: E 38 MET cc_start: 0.2620 (mtt) cc_final: 0.1124 (tmm) REVERT: E 75 MET cc_start: 0.1662 (ttp) cc_final: 0.1175 (ttp) REVERT: E 683 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: F 276 MET cc_start: 0.5136 (mtp) cc_final: 0.4306 (mpp) REVERT: F 347 LYS cc_start: 0.7629 (tptt) cc_final: 0.7270 (tmtt) REVERT: F 372 MET cc_start: 0.8551 (mtm) cc_final: 0.8117 (mtm) REVERT: F 393 HIS cc_start: 0.6778 (m-70) cc_final: 0.6500 (m170) REVERT: F 401 MET cc_start: 0.7875 (tpp) cc_final: 0.7566 (tpt) REVERT: F 485 MET cc_start: 0.7073 (pmt) cc_final: 0.6259 (mmm) REVERT: F 546 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 38 MET cc_start: 0.2010 (tpt) cc_final: 0.0424 (ptt) REVERT: A 75 MET cc_start: -0.1681 (ttt) cc_final: -0.2119 (ttt) REVERT: A 247 GLU cc_start: 0.7633 (mp0) cc_final: 0.7374 (mp0) REVERT: A 255 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7232 (mp0) REVERT: A 308 ILE cc_start: 0.8472 (pt) cc_final: 0.8157 (mt) REVERT: A 328 ARG cc_start: 0.6920 (mpt180) cc_final: 0.6597 (tpp-160) REVERT: A 484 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7322 (mtm-85) REVERT: A 591 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: A 649 GLN cc_start: 0.8568 (pm20) cc_final: 0.8190 (pm20) REVERT: A 660 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8538 (mmmt) outliers start: 88 outliers final: 49 residues processed: 276 average time/residue: 1.6420 time to fit residues: 541.8443 Evaluate side-chains 251 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 194 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 773 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 0.7980 chunk 403 optimal weight: 50.0000 chunk 88 optimal weight: 30.0000 chunk 263 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 448 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 148 optimal weight: 0.0970 chunk 235 optimal weight: 30.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 ASN E 454 HIS F 393 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 37871 Z= 0.155 Angle : 0.565 13.772 51371 Z= 0.277 Chirality : 0.042 0.180 5844 Planarity : 0.005 0.068 6657 Dihedral : 8.108 160.657 5323 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 1.55 % Allowed : 10.81 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4662 helix: 1.22 (0.12), residues: 2050 sheet: -0.12 (0.21), residues: 642 loop : -1.76 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 298 HIS 0.003 0.001 HIS C 377 PHE 0.018 0.001 PHE B 657 TYR 0.014 0.001 TYR F 224 ARG 0.009 0.000 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 215 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1619 (mmt) cc_final: 0.0464 (pmm) REVERT: B 748 LYS cc_start: 0.9043 (mmpt) cc_final: 0.8716 (mppt) REVERT: C 38 MET cc_start: -0.0094 (mmt) cc_final: -0.0401 (mmt) REVERT: C 359 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (m) REVERT: C 385 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7583 (ttp-170) REVERT: C 398 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7944 (mm) REVERT: C 479 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7856 (mmp-170) REVERT: C 586 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7814 (p0) REVERT: D 161 LEU cc_start: -0.0568 (OUTLIER) cc_final: -0.1329 (tp) REVERT: D 401 MET cc_start: 0.8774 (ptt) cc_final: 0.8470 (ptp) REVERT: D 422 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8670 (t0) REVERT: E 38 MET cc_start: 0.2390 (mtt) cc_final: 0.0982 (tmm) REVERT: E 75 MET cc_start: 0.1735 (ttp) cc_final: 0.1272 (ttp) REVERT: E 401 MET cc_start: 0.4869 (ppp) cc_final: 0.4634 (ppp) REVERT: F 53 GLU cc_start: -0.0282 (OUTLIER) cc_final: -0.0716 (mm-30) REVERT: F 276 MET cc_start: 0.5016 (mtp) cc_final: 0.4219 (mpp) REVERT: F 347 LYS cc_start: 0.7611 (tptt) cc_final: 0.7217 (tmtt) REVERT: F 372 MET cc_start: 0.8525 (mtm) cc_final: 0.8015 (mtm) REVERT: F 393 HIS cc_start: 0.6528 (m90) cc_final: 0.6304 (m170) REVERT: F 482 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6354 (tp) REVERT: F 485 MET cc_start: 0.7263 (pmt) cc_final: 0.6397 (mmm) REVERT: A 38 MET cc_start: 0.1949 (tpt) cc_final: 0.0544 (ptt) REVERT: A 75 MET cc_start: -0.1672 (ttt) cc_final: -0.2096 (ttt) REVERT: A 247 GLU cc_start: 0.7964 (mp0) cc_final: 0.7643 (mp0) REVERT: A 255 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7180 (mp0) REVERT: A 308 ILE cc_start: 0.8323 (pt) cc_final: 0.8094 (mm) REVERT: A 591 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 660 LYS cc_start: 0.8774 (mmtm) cc_final: 0.8465 (mmmt) outliers start: 61 outliers final: 23 residues processed: 262 average time/residue: 1.7429 time to fit residues: 546.3748 Evaluate side-chains 235 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 255 optimal weight: 50.0000 chunk 327 optimal weight: 40.0000 chunk 254 optimal weight: 20.0000 chunk 377 optimal weight: 6.9990 chunk 250 optimal weight: 40.0000 chunk 447 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 647 HIS E 93 GLN E 216 GLN E 220 ASN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN A 49 GLN A 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 37871 Z= 0.496 Angle : 0.735 15.255 51371 Z= 0.359 Chirality : 0.049 0.212 5844 Planarity : 0.006 0.076 6657 Dihedral : 8.274 158.331 5323 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 1.88 % Allowed : 11.04 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4662 helix: 1.04 (0.12), residues: 2045 sheet: -0.14 (0.21), residues: 640 loop : -1.75 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 298 HIS 0.011 0.002 HIS B 454 PHE 0.027 0.002 PHE B 466 TYR 0.034 0.002 TYR F 577 ARG 0.008 0.001 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 201 time to evaluate : 4.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1842 (mmt) cc_final: 0.0603 (pmm) REVERT: B 748 LYS cc_start: 0.9025 (mmpt) cc_final: 0.8717 (mppt) REVERT: C 38 MET cc_start: -0.0277 (mmt) cc_final: -0.0814 (mmt) REVERT: C 359 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7232 (m) REVERT: C 586 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7853 (p0) REVERT: D 161 LEU cc_start: -0.0377 (OUTLIER) cc_final: -0.1198 (tp) REVERT: D 405 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8479 (mm) REVERT: D 422 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8744 (t0) REVERT: E 38 MET cc_start: 0.2358 (mtt) cc_final: 0.0885 (tmm) REVERT: E 75 MET cc_start: 0.1661 (ttp) cc_final: 0.1167 (ttp) REVERT: E 683 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8227 (mtt) REVERT: F 53 GLU cc_start: -0.0168 (OUTLIER) cc_final: -0.0821 (mm-30) REVERT: F 276 MET cc_start: 0.5085 (mtp) cc_final: 0.4272 (mpp) REVERT: F 347 LYS cc_start: 0.7495 (tptt) cc_final: 0.7114 (tmtt) REVERT: F 372 MET cc_start: 0.8511 (mtm) cc_final: 0.8078 (mtm) REVERT: F 393 HIS cc_start: 0.6540 (m90) cc_final: 0.6323 (m170) REVERT: F 401 MET cc_start: 0.7973 (tpp) cc_final: 0.7723 (tpt) REVERT: F 482 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6610 (tp) REVERT: F 483 ASP cc_start: 0.8394 (m-30) cc_final: 0.8160 (m-30) REVERT: F 485 MET cc_start: 0.7347 (pmt) cc_final: 0.6709 (mmt) REVERT: A 38 MET cc_start: 0.1974 (tpt) cc_final: 0.0391 (ptt) REVERT: A 75 MET cc_start: -0.1613 (ttt) cc_final: -0.2038 (ttt) REVERT: A 247 GLU cc_start: 0.8007 (mp0) cc_final: 0.7597 (mp0) REVERT: A 255 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7231 (mp0) REVERT: A 308 ILE cc_start: 0.8462 (pt) cc_final: 0.8219 (mt) REVERT: A 328 ARG cc_start: 0.6947 (mpt180) cc_final: 0.6617 (tpp-160) REVERT: A 484 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7301 (mtm-85) REVERT: A 591 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7903 (mp0) outliers start: 74 outliers final: 41 residues processed: 258 average time/residue: 1.6637 time to fit residues: 516.6118 Evaluate side-chains 243 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 20.0000 chunk 178 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 284 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 221 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 351 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 ASN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37871 Z= 0.163 Angle : 0.571 12.455 51371 Z= 0.279 Chirality : 0.042 0.177 5844 Planarity : 0.005 0.070 6657 Dihedral : 8.004 158.063 5323 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 1.50 % Allowed : 11.63 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4662 helix: 1.40 (0.12), residues: 2039 sheet: 0.10 (0.21), residues: 633 loop : -1.66 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 298 HIS 0.003 0.001 HIS D 139 PHE 0.019 0.001 PHE B 657 TYR 0.013 0.001 TYR F 224 ARG 0.006 0.000 ARG E 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 196 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.1779 (mmt) cc_final: 0.0555 (pmm) REVERT: B 748 LYS cc_start: 0.9024 (mmpt) cc_final: 0.8718 (mppt) REVERT: C 38 MET cc_start: -0.0294 (mmt) cc_final: -0.0777 (mmt) REVERT: C 385 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7670 (ttp-170) REVERT: C 398 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 479 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7846 (mmp-170) REVERT: C 586 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7804 (p0) REVERT: C 713 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: D 161 LEU cc_start: -0.0535 (OUTLIER) cc_final: -0.1160 (tp) REVERT: D 401 MET cc_start: 0.8795 (ptt) cc_final: 0.8488 (ptp) REVERT: E 38 MET cc_start: 0.2267 (mtt) cc_final: 0.0824 (tmm) REVERT: E 75 MET cc_start: 0.1463 (ttp) cc_final: 0.1033 (ttp) REVERT: E 217 MET cc_start: 0.3588 (tmm) cc_final: 0.3319 (pp-130) REVERT: E 276 MET cc_start: -0.0845 (ptt) cc_final: -0.1052 (ptt) REVERT: E 394 ARG cc_start: 0.5386 (tpp80) cc_final: 0.4784 (mmm-85) REVERT: E 401 MET cc_start: 0.4986 (ppp) cc_final: 0.4711 (ppp) REVERT: F 53 GLU cc_start: -0.0315 (OUTLIER) cc_final: -0.0774 (mm-30) REVERT: F 276 MET cc_start: 0.4954 (mtp) cc_final: 0.4136 (mpp) REVERT: F 347 LYS cc_start: 0.7471 (tptt) cc_final: 0.7112 (tmtt) REVERT: F 372 MET cc_start: 0.8533 (mtm) cc_final: 0.8050 (mtm) REVERT: F 393 HIS cc_start: 0.6504 (m90) cc_final: 0.6292 (m170) REVERT: F 401 MET cc_start: 0.7981 (tpp) cc_final: 0.7762 (tpt) REVERT: F 483 ASP cc_start: 0.8320 (m-30) cc_final: 0.7680 (p0) REVERT: F 485 MET cc_start: 0.7354 (pmt) cc_final: 0.6712 (mmt) REVERT: A 38 MET cc_start: 0.1894 (tpt) cc_final: 0.0461 (ptt) REVERT: A 75 MET cc_start: -0.1748 (ttt) cc_final: -0.2146 (ttt) REVERT: A 247 GLU cc_start: 0.7993 (mp0) cc_final: 0.7672 (mp0) REVERT: A 484 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7159 (mtm-85) REVERT: A 591 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7818 (mp0) outliers start: 59 outliers final: 24 residues processed: 243 average time/residue: 1.6965 time to fit residues: 497.2945 Evaluate side-chains 222 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 30.0000 chunk 428 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 416 optimal weight: 7.9990 chunk 250 optimal weight: 50.0000 chunk 181 optimal weight: 0.8980 chunk 327 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 376 optimal weight: 10.0000 chunk 394 optimal weight: 4.9990 chunk 415 optimal weight: 0.0070 overall best weight: 3.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37871 Z= 0.321 Angle : 0.645 15.552 51371 Z= 0.313 Chirality : 0.045 0.190 5844 Planarity : 0.005 0.071 6657 Dihedral : 7.989 155.797 5323 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 1.35 % Allowed : 11.96 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 4662 helix: 1.38 (0.12), residues: 2041 sheet: 0.11 (0.21), residues: 638 loop : -1.66 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.007 0.001 HIS B 454 PHE 0.019 0.001 PHE B 466 TYR 0.021 0.001 TYR F 577 ARG 0.011 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.2194 (mmt) cc_final: 0.0813 (pmm) REVERT: B 439 MET cc_start: 0.9112 (mmm) cc_final: 0.8911 (mmt) REVERT: B 748 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8713 (mppt) REVERT: C 38 MET cc_start: -0.0259 (mmt) cc_final: -0.0758 (mmt) REVERT: C 385 ARG cc_start: 0.8093 (ttp-170) cc_final: 0.7820 (ttp-170) REVERT: C 586 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7834 (p0) REVERT: D 161 LEU cc_start: -0.0527 (OUTLIER) cc_final: -0.1110 (tp) REVERT: D 422 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8748 (t0) REVERT: E 38 MET cc_start: 0.2300 (mtt) cc_final: 0.0857 (tmm) REVERT: E 75 MET cc_start: 0.1551 (ttp) cc_final: 0.1104 (ttp) REVERT: E 217 MET cc_start: 0.3692 (tmm) cc_final: 0.3175 (ppp) REVERT: E 394 ARG cc_start: 0.5549 (tpp80) cc_final: 0.4881 (mmm-85) REVERT: E 401 MET cc_start: 0.5012 (ppp) cc_final: 0.4765 (ppp) REVERT: E 683 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: F 53 GLU cc_start: -0.0222 (OUTLIER) cc_final: -0.0803 (mm-30) REVERT: F 85 MET cc_start: 0.2380 (tmm) cc_final: 0.1896 (tpp) REVERT: F 276 MET cc_start: 0.5007 (mtp) cc_final: 0.4187 (mpp) REVERT: F 347 LYS cc_start: 0.7427 (tptt) cc_final: 0.7165 (tptt) REVERT: F 372 MET cc_start: 0.8519 (mtm) cc_final: 0.8083 (mtm) REVERT: F 393 HIS cc_start: 0.6504 (m90) cc_final: 0.6292 (m170) REVERT: F 401 MET cc_start: 0.7985 (tpp) cc_final: 0.7733 (tpt) REVERT: F 485 MET cc_start: 0.7363 (pmt) cc_final: 0.6538 (mmt) REVERT: A 38 MET cc_start: 0.1883 (tpt) cc_final: 0.0472 (mtm) REVERT: A 75 MET cc_start: -0.1670 (ttt) cc_final: -0.2080 (ttt) REVERT: A 247 GLU cc_start: 0.8058 (mp0) cc_final: 0.7629 (mp0) REVERT: A 255 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7231 (mp0) REVERT: A 328 ARG cc_start: 0.6881 (mpt180) cc_final: 0.6548 (tpp-160) REVERT: A 484 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7262 (mtm-85) REVERT: A 591 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7855 (mp0) outliers start: 53 outliers final: 29 residues processed: 234 average time/residue: 1.7203 time to fit residues: 480.5658 Evaluate side-chains 225 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 4.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 20.0000 chunk 440 optimal weight: 0.9990 chunk 268 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 462 optimal weight: 30.0000 chunk 425 optimal weight: 6.9990 chunk 368 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 chunk 225 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37871 Z= 0.250 Angle : 0.600 13.334 51371 Z= 0.292 Chirality : 0.044 0.176 5844 Planarity : 0.005 0.071 6657 Dihedral : 7.926 154.651 5323 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 1.07 % Allowed : 12.26 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4662 helix: 1.46 (0.12), residues: 2042 sheet: 0.15 (0.21), residues: 635 loop : -1.60 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 298 HIS 0.004 0.001 HIS A 454 PHE 0.021 0.001 PHE E 466 TYR 0.015 0.001 TYR F 577 ARG 0.008 0.000 ARG B 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 4.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.2262 (mmt) cc_final: 0.0869 (pmm) REVERT: B 748 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8708 (mppt) REVERT: C 38 MET cc_start: -0.0318 (mmt) cc_final: -0.0778 (mmt) REVERT: C 385 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7818 (ttp-170) REVERT: C 398 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7946 (mm) REVERT: C 586 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7828 (p0) REVERT: D 161 LEU cc_start: -0.0553 (OUTLIER) cc_final: -0.1045 (tp) REVERT: D 422 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8748 (t0) REVERT: E 38 MET cc_start: 0.2085 (mtt) cc_final: 0.0747 (tmm) REVERT: E 75 MET cc_start: 0.1559 (ttp) cc_final: 0.1112 (ttp) REVERT: E 217 MET cc_start: 0.3793 (tmm) cc_final: 0.3328 (ppp) REVERT: E 394 ARG cc_start: 0.5548 (tpp80) cc_final: 0.4885 (mmm-85) REVERT: E 401 MET cc_start: 0.5077 (ppp) cc_final: 0.4827 (ppp) REVERT: F 53 GLU cc_start: -0.0336 (OUTLIER) cc_final: -0.0801 (mm-30) REVERT: F 85 MET cc_start: 0.2333 (tmm) cc_final: 0.1859 (tpp) REVERT: F 276 MET cc_start: 0.5010 (mtp) cc_final: 0.4120 (mpp) REVERT: F 372 MET cc_start: 0.8528 (mtm) cc_final: 0.8073 (mtm) REVERT: F 393 HIS cc_start: 0.6480 (m90) cc_final: 0.6269 (m170) REVERT: F 401 MET cc_start: 0.7984 (tpp) cc_final: 0.7738 (tpt) REVERT: F 485 MET cc_start: 0.7418 (pmt) cc_final: 0.6528 (mmt) REVERT: A 38 MET cc_start: 0.1777 (tpt) cc_final: 0.0341 (mtm) REVERT: A 75 MET cc_start: -0.1590 (ttt) cc_final: -0.1962 (ttt) REVERT: A 247 GLU cc_start: 0.8039 (mp0) cc_final: 0.7634 (mp0) REVERT: A 484 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7239 (mtm-85) REVERT: A 591 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7853 (mp0) outliers start: 42 outliers final: 28 residues processed: 224 average time/residue: 1.8046 time to fit residues: 482.2012 Evaluate side-chains 221 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 225 TYR Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 2.9990 chunk 392 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 368 optimal weight: 0.6980 chunk 154 optimal weight: 30.0000 chunk 378 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 GLN E 93 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.179271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107365 restraints weight = 66130.658| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.95 r_work: 0.2992 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37871 Z= 0.142 Angle : 0.549 12.604 51371 Z= 0.265 Chirality : 0.041 0.178 5844 Planarity : 0.004 0.068 6657 Dihedral : 7.684 150.529 5323 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 0.99 % Allowed : 12.29 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 4662 helix: 1.75 (0.12), residues: 2025 sheet: 0.23 (0.21), residues: 638 loop : -1.46 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 298 HIS 0.003 0.000 HIS D 139 PHE 0.014 0.001 PHE B 657 TYR 0.015 0.001 TYR F 224 ARG 0.007 0.000 ARG A 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13337.50 seconds wall clock time: 239 minutes 22.62 seconds (14362.62 seconds total)