Starting phenix.real_space_refine on Thu May 16 12:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqa_37736/05_2024/8wqa_37736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqa_37736/05_2024/8wqa_37736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqa_37736/05_2024/8wqa_37736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqa_37736/05_2024/8wqa_37736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqa_37736/05_2024/8wqa_37736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqa_37736/05_2024/8wqa_37736.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7310 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 182 5.16 5 C 16744 2.51 5 N 4594 2.21 5 O 4953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "I GLU 100": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 26479 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "F" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 8, 'TRANS': 86} Chain breaks: 1 Chain: "J" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 677 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 674 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4930 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12659 SG CYS J 53 50.156 86.190 57.202 1.00 56.35 S ATOM 12682 SG CYS J 56 50.622 83.417 54.506 1.00 66.76 S ATOM 12766 SG CYS J 68 49.019 86.609 53.550 1.00 54.99 S ATOM 12573 SG CYS J 42 51.941 92.902 58.560 1.00 30.52 S ATOM 12592 SG CYS J 45 53.994 89.879 59.735 1.00 30.89 S ATOM 12887 SG CYS J 83 50.304 89.460 59.275 1.00 36.37 S ATOM 12816 SG CYS J 75 46.610 104.746 59.586 1.00 46.47 S ATOM 12983 SG CYS J 94 46.825 102.419 62.065 1.00 42.31 S ATOM 14855 SG CYS I 53 50.174 48.755 156.221 1.00 38.61 S ATOM 14878 SG CYS I 56 48.331 51.601 158.006 1.00 48.27 S ATOM 14962 SG CYS I 68 50.224 48.989 160.043 1.00 48.67 S ATOM 14769 SG CYS I 42 51.950 41.630 153.269 1.00 23.19 S ATOM 14788 SG CYS I 45 53.929 44.894 153.004 1.00 24.22 S ATOM 15080 SG CYS I 83 50.151 45.107 152.961 1.00 27.07 S ATOM 15012 SG CYS I 75 46.885 31.109 153.020 1.00 34.64 S ATOM 15176 SG CYS I 94 47.218 32.837 150.283 1.00 32.67 S Time building chain proxies: 13.02, per 1000 atoms: 0.49 Number of scatterers: 26479 At special positions: 0 Unit cell: (118.08, 136.12, 213.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 182 16.00 O 4953 8.00 N 4594 7.00 C 16744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 56 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 53 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 42 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 75 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " Number of angles added : 12 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6350 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 16 sheets defined 62.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'C' and resid 9 through 26 removed outlier: 3.686A pdb=" N THR C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.829A pdb=" N PHE C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 78 removed outlier: 3.516A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 removed outlier: 3.949A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.501A pdb=" N LEU C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 173 removed outlier: 3.673A pdb=" N ILE C 160 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 removed outlier: 3.828A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 207 through 228 removed outlier: 3.864A pdb=" N GLN C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 3.793A pdb=" N MET C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.710A pdb=" N TYR C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C 260 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.570A pdb=" N ARG C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.908A pdb=" N HIS C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.829A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 357 removed outlier: 4.059A pdb=" N VAL C 340 " --> pdb=" O PRO C 336 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 377 Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 407 through 423 removed outlier: 3.917A pdb=" N ASP C 413 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.638A pdb=" N PHE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 470 removed outlier: 7.481A pdb=" N TYR C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N GLU C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 469 " --> pdb=" O CYS C 465 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 494 removed outlier: 4.024A pdb=" N TYR C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 492 " --> pdb=" O ASN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 548 removed outlier: 4.204A pdb=" N LYS C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 591 removed outlier: 3.885A pdb=" N LEU C 585 " --> pdb=" O GLN C 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE C 588 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.675A pdb=" N THR C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 619 removed outlier: 4.695A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 Processing helix chain 'C' and resid 661 through 692 removed outlier: 3.663A pdb=" N ARG C 669 " --> pdb=" O MET C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 714 through 728 removed outlier: 3.751A pdb=" N ILE C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 719 " --> pdb=" O ILE C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 15 removed outlier: 3.708A pdb=" N GLY D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.810A pdb=" N ALA D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.588A pdb=" N ARG D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'D' and resid 123 through 131 removed outlier: 3.634A pdb=" N ALA D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.764A pdb=" N ILE D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.964A pdb=" N LYS D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 233 through 241 removed outlier: 4.332A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.527A pdb=" N ASN D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.810A pdb=" N ARG D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.584A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 337 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.140A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 378 Processing helix chain 'D' and resid 381 through 398 Processing helix chain 'D' and resid 403 through 427 Processing helix chain 'D' and resid 432 through 457 Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 548 through 562 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 596 through 608 Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.937A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'E' and resid 66 through 84 removed outlier: 4.155A pdb=" N LYS E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'F' and resid 23 through 36 removed outlier: 4.070A pdb=" N LEU F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.695A pdb=" N GLY F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 66 through 83 removed outlier: 3.732A pdb=" N LYS G 72 " --> pdb=" O HIS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.260A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.596A pdb=" N GLY H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 3.929A pdb=" N ALA I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 91 removed outlier: 4.148A pdb=" N THR I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.693A pdb=" N ASN A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.824A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.993A pdb=" N HIS A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.931A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.991A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.752A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 228 removed outlier: 4.144A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.414A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.664A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.595A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.694A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.873A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.593A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 423 removed outlier: 4.005A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.717A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 removed outlier: 7.476A pdb=" N TYR A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 494 removed outlier: 4.465A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 547 removed outlier: 4.435A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.883A pdb=" N LEU A 569 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 581 through 591 removed outlier: 3.628A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 604 removed outlier: 4.146A pdb=" N ASP A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 619 removed outlier: 3.694A pdb=" N LEU A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.564A pdb=" N LYS A 659 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 removed outlier: 3.901A pdb=" N MET A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 removed outlier: 3.878A pdb=" N ILE A 700 " --> pdb=" O HIS A 696 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 3.568A pdb=" N GLU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.801A pdb=" N HIS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.547A pdb=" N CYS B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.790A pdb=" N LYS B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.748A pdb=" N VAL B 170 " --> pdb=" O HIS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.718A pdb=" N PHE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.703A pdb=" N SER B 240 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 262 removed outlier: 3.520A pdb=" N ASN B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.532A pdb=" N GLY B 303 " --> pdb=" O HIS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.562A pdb=" N ILE B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 337 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.931A pdb=" N ILE B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 Processing helix chain 'B' and resid 381 through 398 Processing helix chain 'B' and resid 403 through 426 Processing helix chain 'B' and resid 432 through 457 Processing helix chain 'B' and resid 460 through 478 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.505A pdb=" N THR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 548 through 562 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 596 through 609 Processing helix chain 'B' and resid 617 through 626 removed outlier: 3.599A pdb=" N GLU B 622 " --> pdb=" O ARG B 618 " (cutoff:3.500A) Processing helix chain 'K' and resid -22 through -17 Processing helix chain 'K' and resid -14 through -5 removed outlier: 3.906A pdb=" N ARG K -5 " --> pdb=" O ASN K -9 " (cutoff:3.500A) Processing helix chain 'L' and resid -13 through -3 removed outlier: 4.144A pdb=" N HIS L -4 " --> pdb=" O GLY L -8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 506 through 507 removed outlier: 5.563A pdb=" N SER C 506 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU J 23 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU C 563 " --> pdb=" O LYS J 25 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP J 27 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR C 561 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 564 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA C 575 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 574 " --> pdb=" O PHE C 651 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 510 through 513 removed outlier: 3.601A pdb=" N ALA J 31 " --> pdb=" O TYR C 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'C' and resid 693 through 695 removed outlier: 3.577A pdb=" N LEU C 694 " --> pdb=" O TYR C 741 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.891A pdb=" N GLY D 77 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 86 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.804A pdb=" N LEU E 21 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE E 30 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N ASP F 17 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N LYS E 32 " --> pdb=" O ASP F 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 41 through 42 removed outlier: 3.516A pdb=" N ASN J 47 " --> pdb=" O CYS J 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 31 through 32 removed outlier: 8.016A pdb=" N VAL G 60 " --> pdb=" O TYR G 18 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS G 20 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 13 through 18 removed outlier: 7.513A pdb=" N PHE H 4 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL H 75 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET H 6 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU H 77 " --> pdb=" O MET H 6 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG H 8 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE H 79 " --> pdb=" O ARG H 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA H 78 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG H 43 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 506 through 507 removed outlier: 3.529A pdb=" N SER A 506 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU I 23 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 563 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP I 27 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 561 " --> pdb=" O TRP I 27 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 564 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA A 575 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 574 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 510 through 513 Processing sheet with id=AB4, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 695 removed outlier: 3.869A pdb=" N LEU A 694 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 742 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 732 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 40 through 42 1365 hydrogen bonds defined for protein. 4029 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: 9.44 Time building geometry restraints manager: 10.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8780 1.34 - 1.46: 5901 1.46 - 1.58: 12020 1.58 - 1.70: 0 1.70 - 1.82: 284 Bond restraints: 26985 Sorted by residual: bond pdb=" C THR A 654 " pdb=" O THR A 654 " ideal model delta sigma weight residual 1.234 1.263 -0.029 1.55e-02 4.16e+03 3.41e+00 bond pdb=" CG1 ILE D 475 " pdb=" CD1 ILE D 475 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.76e+00 bond pdb=" SD MET A 457 " pdb=" CE MET A 457 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CA ASP A 660 " pdb=" C ASP A 660 " ideal model delta sigma weight residual 1.526 1.513 0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" N THR A 654 " pdb=" CA THR A 654 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.15e-02 7.56e+03 1.37e+00 ... (remaining 26980 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.69: 366 104.69 - 112.01: 13143 112.01 - 119.33: 9503 119.33 - 126.65: 13141 126.65 - 133.97: 320 Bond angle restraints: 36473 Sorted by residual: angle pdb=" N THR A 655 " pdb=" CA THR A 655 " pdb=" C THR A 655 " ideal model delta sigma weight residual 111.36 105.43 5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N THR C 655 " pdb=" CA THR C 655 " pdb=" C THR C 655 " ideal model delta sigma weight residual 111.75 105.79 5.96 1.28e+00 6.10e-01 2.17e+01 angle pdb=" C LYS F 46 " pdb=" N ASP F 47 " pdb=" CA ASP F 47 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA MET A 717 " pdb=" CB MET A 717 " pdb=" CG MET A 717 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA MET E 17 " pdb=" CB MET E 17 " pdb=" CG MET E 17 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 ... (remaining 36468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14613 17.89 - 35.78: 1467 35.78 - 53.68: 273 53.68 - 71.57: 51 71.57 - 89.46: 22 Dihedral angle restraints: 16426 sinusoidal: 6665 harmonic: 9761 Sorted by residual: dihedral pdb=" CA ASN J 76 " pdb=" C ASN J 76 " pdb=" N HIS J 77 " pdb=" CA HIS J 77 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LYS A 621 " pdb=" C LYS A 621 " pdb=" N MET A 622 " pdb=" CA MET A 622 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA MET D 595 " pdb=" C MET D 595 " pdb=" N SER D 596 " pdb=" CA SER D 596 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 16423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2710 0.037 - 0.074: 1071 0.074 - 0.111: 246 0.111 - 0.148: 66 0.148 - 0.184: 12 Chirality restraints: 4105 Sorted by residual: chirality pdb=" CB ILE B 347 " pdb=" CA ILE B 347 " pdb=" CG1 ILE B 347 " pdb=" CG2 ILE B 347 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CG LEU C 559 " pdb=" CB LEU C 559 " pdb=" CD1 LEU C 559 " pdb=" CD2 LEU C 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CB ILE G 90 " pdb=" CA ILE G 90 " pdb=" CG1 ILE G 90 " pdb=" CG2 ILE G 90 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 4102 not shown) Planarity restraints: 4685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 96 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO E 97 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 558 " 0.015 2.00e-02 2.50e+03 1.62e-02 5.27e+00 pdb=" CG TYR C 558 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR C 558 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 558 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR C 558 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 558 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 558 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 558 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 94 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO I 95 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " -0.031 5.00e-02 4.00e+02 ... (remaining 4682 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 292 2.63 - 3.20: 24353 3.20 - 3.76: 43509 3.76 - 4.33: 57546 4.33 - 4.90: 94232 Nonbonded interactions: 219932 Sorted by model distance: nonbonded pdb=" CD2 HIS J 77 " pdb="ZN ZN J 202 " model vdw 2.059 1.960 nonbonded pdb=" OD1 ASP D 499 " pdb=" OG1 THR D 503 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR C 219 " pdb=" OE1 GLU C 246 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASN A 624 " pdb=" OG SER A 639 " model vdw 2.210 2.440 nonbonded pdb=" OG1 THR B 167 " pdb=" OD2 ASP B 201 " model vdw 2.223 2.440 ... (remaining 219927 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 626 or (resid 627 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2)))) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 2 through 80 or resid 85 through 100)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 22 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 104 or resid 200 through 202)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 9.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 30.640 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 72.040 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26985 Z= 0.206 Angle : 0.640 9.912 36473 Z= 0.346 Chirality : 0.042 0.184 4105 Planarity : 0.004 0.073 4685 Dihedral : 14.891 89.460 10076 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.14 % Allowed : 0.38 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3269 helix: 0.16 (0.12), residues: 1870 sheet: -0.69 (0.57), residues: 89 loop : -1.27 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 367 HIS 0.006 0.001 HIS J 77 PHE 0.037 0.002 PHE D 392 TYR 0.040 0.002 TYR C 558 ARG 0.011 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 3.097 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: C 151 MET cc_start: 0.8876 (tpp) cc_final: 0.7937 (tpt) REVERT: C 538 GLN cc_start: 0.8100 (tp40) cc_final: 0.7419 (pp30) REVERT: A 605 MET cc_start: 0.6007 (pmm) cc_final: 0.5493 (pmm) REVERT: K -3 LEU cc_start: 0.7321 (pp) cc_final: 0.7037 (mp) outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 0.3593 time to fit residues: 182.0973 Evaluate side-chains 260 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 253 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 154 optimal weight: 0.0370 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26985 Z= 0.214 Angle : 0.534 8.608 36473 Z= 0.280 Chirality : 0.040 0.151 4105 Planarity : 0.004 0.057 4685 Dihedral : 4.356 71.486 3585 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.65 % Allowed : 7.11 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3269 helix: 0.62 (0.12), residues: 1944 sheet: -0.83 (0.56), residues: 89 loop : -1.17 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 367 HIS 0.005 0.001 HIS C 88 PHE 0.022 0.001 PHE D 392 TYR 0.027 0.001 TYR C 558 ARG 0.005 0.000 ARG L -5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 275 time to evaluate : 2.966 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: C 151 MET cc_start: 0.8924 (tpp) cc_final: 0.8281 (tpt) REVERT: C 294 MET cc_start: 0.7657 (mtm) cc_final: 0.7365 (mtm) REVERT: E 18 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7390 (t80) REVERT: A 605 MET cc_start: 0.6465 (pmm) cc_final: 0.5275 (pmm) REVERT: K -3 LEU cc_start: 0.7153 (pp) cc_final: 0.6861 (mp) outliers start: 19 outliers final: 13 residues processed: 284 average time/residue: 0.3665 time to fit residues: 169.1658 Evaluate side-chains 274 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 260 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain H residue 25 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 544 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 318 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 292 optimal weight: 0.0470 chunk 100 optimal weight: 0.3980 chunk 236 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN A 508 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26985 Z= 0.170 Angle : 0.498 9.209 36473 Z= 0.258 Chirality : 0.039 0.257 4105 Planarity : 0.004 0.051 4685 Dihedral : 4.200 71.058 3584 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.96 % Allowed : 9.54 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3269 helix: 0.82 (0.12), residues: 1965 sheet: -0.84 (0.57), residues: 89 loop : -1.14 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 87 HIS 0.005 0.001 HIS J 77 PHE 0.019 0.001 PHE B 130 TYR 0.023 0.001 TYR D 163 ARG 0.006 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 3.103 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: C 151 MET cc_start: 0.8909 (tpp) cc_final: 0.8134 (tpt) REVERT: C 451 MET cc_start: 0.8039 (mmp) cc_final: 0.7827 (mmp) REVERT: C 477 TYR cc_start: 0.8004 (t80) cc_final: 0.7792 (t80) REVERT: C 539 MET cc_start: 0.6741 (tmm) cc_final: 0.6503 (ttt) REVERT: A 605 MET cc_start: 0.6676 (pmm) cc_final: 0.5459 (pmm) REVERT: K -3 LEU cc_start: 0.7147 (pp) cc_final: 0.6805 (mp) outliers start: 28 outliers final: 23 residues processed: 293 average time/residue: 0.3748 time to fit residues: 178.1707 Evaluate side-chains 288 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 265 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.0370 chunk 221 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 197 optimal weight: 0.0980 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 154 optimal weight: 0.0030 chunk 280 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 overall best weight: 0.2268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN C 667 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26985 Z= 0.127 Angle : 0.482 10.168 36473 Z= 0.248 Chirality : 0.038 0.235 4105 Planarity : 0.003 0.048 4685 Dihedral : 4.070 71.419 3584 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.17 % Allowed : 11.50 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3269 helix: 1.01 (0.12), residues: 1968 sheet: -0.82 (0.58), residues: 89 loop : -1.09 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 87 HIS 0.004 0.001 HIS D 345 PHE 0.028 0.001 PHE A 112 TYR 0.029 0.001 TYR C 558 ARG 0.008 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 289 time to evaluate : 2.982 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: C 151 MET cc_start: 0.8861 (tpp) cc_final: 0.8074 (tpt) REVERT: C 338 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8633 (tp) REVERT: C 447 LEU cc_start: 0.8656 (mm) cc_final: 0.8450 (mt) REVERT: C 451 MET cc_start: 0.7959 (mmp) cc_final: 0.7579 (mmp) REVERT: C 477 TYR cc_start: 0.7998 (t80) cc_final: 0.7752 (t80) REVERT: C 538 GLN cc_start: 0.8071 (tp40) cc_final: 0.7310 (pp30) REVERT: A 547 HIS cc_start: 0.6665 (t70) cc_final: 0.6433 (t70) REVERT: A 605 MET cc_start: 0.6713 (pmm) cc_final: 0.5656 (pmm) REVERT: A 657 MET cc_start: 0.4766 (OUTLIER) cc_final: 0.4510 (tpt) REVERT: B 193 PHE cc_start: 0.8659 (m-10) cc_final: 0.8436 (m-80) REVERT: K -3 LEU cc_start: 0.7315 (pp) cc_final: 0.6968 (mp) outliers start: 34 outliers final: 20 residues processed: 305 average time/residue: 0.3762 time to fit residues: 186.0306 Evaluate side-chains 289 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 267 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 267 optimal weight: 20.0000 chunk 216 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26985 Z= 0.212 Angle : 0.516 10.098 36473 Z= 0.264 Chirality : 0.039 0.200 4105 Planarity : 0.003 0.049 4685 Dihedral : 4.035 67.442 3584 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.58 % Allowed : 12.08 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3269 helix: 1.01 (0.12), residues: 1968 sheet: -0.96 (0.56), residues: 89 loop : -1.05 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.006 0.001 HIS C 88 PHE 0.022 0.001 PHE A 112 TYR 0.015 0.001 TYR D 472 ARG 0.007 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 273 time to evaluate : 3.042 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: C 151 MET cc_start: 0.8923 (tpp) cc_final: 0.8151 (tpt) REVERT: C 447 LEU cc_start: 0.8683 (mm) cc_final: 0.8416 (mt) REVERT: C 451 MET cc_start: 0.8076 (mmp) cc_final: 0.7678 (mmp) REVERT: C 538 GLN cc_start: 0.8102 (tp40) cc_final: 0.7385 (pp30) REVERT: A 236 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7101 (mpp) REVERT: A 547 HIS cc_start: 0.6736 (t70) cc_final: 0.6487 (t70) REVERT: A 605 MET cc_start: 0.6820 (pmm) cc_final: 0.5760 (pmm) REVERT: A 657 MET cc_start: 0.4728 (OUTLIER) cc_final: 0.4390 (tpt) REVERT: A 677 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8462 (mmtp) REVERT: B 193 PHE cc_start: 0.8663 (m-10) cc_final: 0.8461 (m-80) REVERT: K -3 LEU cc_start: 0.7327 (pp) cc_final: 0.6955 (mp) outliers start: 46 outliers final: 33 residues processed: 295 average time/residue: 0.3829 time to fit residues: 184.7673 Evaluate side-chains 299 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 164 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26985 Z= 0.171 Angle : 0.498 12.531 36473 Z= 0.255 Chirality : 0.038 0.201 4105 Planarity : 0.003 0.049 4685 Dihedral : 4.002 67.811 3584 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.09 % Allowed : 12.15 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3269 helix: 1.08 (0.12), residues: 1974 sheet: -0.96 (0.56), residues: 89 loop : -1.06 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 367 HIS 0.004 0.001 HIS D 100 PHE 0.020 0.001 PHE B 130 TYR 0.037 0.001 TYR C 558 ARG 0.006 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 272 time to evaluate : 3.115 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: C 151 MET cc_start: 0.8898 (tpp) cc_final: 0.8086 (tpt) REVERT: C 447 LEU cc_start: 0.8661 (mm) cc_final: 0.8446 (mt) REVERT: C 451 MET cc_start: 0.8081 (mmp) cc_final: 0.7791 (mmp) REVERT: F 52 ASP cc_start: 0.6301 (p0) cc_final: 0.6082 (p0) REVERT: G 17 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6582 (ttm) REVERT: A 236 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.6990 (mpp) REVERT: A 547 HIS cc_start: 0.6734 (t70) cc_final: 0.6490 (t70) REVERT: A 605 MET cc_start: 0.6888 (pmm) cc_final: 0.5801 (pmm) REVERT: A 657 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.4347 (tpt) REVERT: A 677 LYS cc_start: 0.8739 (tmtt) cc_final: 0.8460 (tptt) REVERT: B 193 PHE cc_start: 0.8657 (m-10) cc_final: 0.8426 (m-80) REVERT: K -3 LEU cc_start: 0.7254 (pp) cc_final: 0.6903 (mp) outliers start: 61 outliers final: 38 residues processed: 308 average time/residue: 0.3677 time to fit residues: 186.2016 Evaluate side-chains 307 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 266 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 263 optimal weight: 50.0000 chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 0.0670 chunk 195 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26985 Z= 0.181 Angle : 0.510 11.532 36473 Z= 0.260 Chirality : 0.039 0.212 4105 Planarity : 0.003 0.049 4685 Dihedral : 3.994 67.416 3584 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.89 % Allowed : 13.04 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3269 helix: 1.10 (0.12), residues: 1982 sheet: -1.04 (0.56), residues: 89 loop : -1.07 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 367 HIS 0.005 0.001 HIS K -21 PHE 0.022 0.001 PHE D 392 TYR 0.027 0.001 TYR B 139 ARG 0.007 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 3.507 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: C 151 MET cc_start: 0.8897 (tpp) cc_final: 0.8077 (tpt) REVERT: C 451 MET cc_start: 0.8093 (mmp) cc_final: 0.7773 (mmp) REVERT: C 538 GLN cc_start: 0.8135 (tp40) cc_final: 0.7395 (pp30) REVERT: F 52 ASP cc_start: 0.6281 (p0) cc_final: 0.6072 (p0) REVERT: G 17 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6567 (ttm) REVERT: A 236 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: A 547 HIS cc_start: 0.6799 (t70) cc_final: 0.6541 (t70) REVERT: A 605 MET cc_start: 0.6909 (pmm) cc_final: 0.5807 (pmm) REVERT: A 657 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4318 (tpt) REVERT: A 677 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8486 (tptt) REVERT: B 193 PHE cc_start: 0.8656 (m-10) cc_final: 0.8437 (m-80) REVERT: K -3 LEU cc_start: 0.7206 (pp) cc_final: 0.6857 (mp) outliers start: 55 outliers final: 42 residues processed: 302 average time/residue: 0.3838 time to fit residues: 192.1704 Evaluate side-chains 309 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 186 optimal weight: 0.0970 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 581 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26985 Z= 0.252 Angle : 0.541 11.756 36473 Z= 0.278 Chirality : 0.040 0.214 4105 Planarity : 0.003 0.050 4685 Dihedral : 4.053 65.800 3584 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.03 % Allowed : 13.18 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3269 helix: 1.04 (0.12), residues: 1974 sheet: -1.18 (0.54), residues: 90 loop : -1.08 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.007 0.001 HIS C 88 PHE 0.021 0.001 PHE B 626 TYR 0.020 0.001 TYR B 139 ARG 0.008 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 267 time to evaluate : 2.907 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: C 151 MET cc_start: 0.8923 (tpp) cc_final: 0.8142 (tpt) REVERT: C 365 MET cc_start: 0.8558 (mmt) cc_final: 0.8274 (mmt) REVERT: C 451 MET cc_start: 0.8225 (mmp) cc_final: 0.7898 (mmp) REVERT: C 480 MET cc_start: 0.8177 (mmm) cc_final: 0.7774 (mmm) REVERT: F 52 ASP cc_start: 0.6355 (p0) cc_final: 0.6144 (p0) REVERT: G 17 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6603 (ttm) REVERT: A 236 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7499 (mpp) REVERT: A 547 HIS cc_start: 0.6859 (t70) cc_final: 0.6581 (t70) REVERT: A 605 MET cc_start: 0.7010 (pmm) cc_final: 0.5925 (pmm) REVERT: A 657 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4353 (tpt) REVERT: A 677 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8514 (tptt) REVERT: B 193 PHE cc_start: 0.8651 (m-10) cc_final: 0.8421 (m-80) REVERT: K -3 LEU cc_start: 0.7191 (pp) cc_final: 0.6831 (mp) outliers start: 59 outliers final: 43 residues processed: 300 average time/residue: 0.3767 time to fit residues: 185.1413 Evaluate side-chains 308 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 262 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 291 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 228 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 262 optimal weight: 0.3980 chunk 275 optimal weight: 7.9990 chunk 289 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 581 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26985 Z= 0.161 Angle : 0.528 14.476 36473 Z= 0.268 Chirality : 0.039 0.229 4105 Planarity : 0.003 0.048 4685 Dihedral : 4.036 69.277 3584 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.68 % Allowed : 13.94 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3269 helix: 1.12 (0.12), residues: 1980 sheet: -1.10 (0.56), residues: 89 loop : -1.07 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 367 HIS 0.010 0.001 HIS D 476 PHE 0.033 0.001 PHE D 193 TYR 0.036 0.001 TYR B 139 ARG 0.007 0.000 ARG L -5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 272 time to evaluate : 3.110 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: C 151 MET cc_start: 0.8856 (tpp) cc_final: 0.8182 (tpt) REVERT: C 365 MET cc_start: 0.8523 (mmt) cc_final: 0.8232 (mmt) REVERT: C 451 MET cc_start: 0.8181 (mmp) cc_final: 0.7857 (mmp) REVERT: C 480 MET cc_start: 0.8079 (mmm) cc_final: 0.7692 (mmm) REVERT: F 91 GLU cc_start: 0.6842 (tp30) cc_final: 0.6609 (tp30) REVERT: G 17 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6551 (ttm) REVERT: A 151 MET cc_start: 0.9023 (tpt) cc_final: 0.8746 (tpt) REVERT: A 236 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7034 (mpp) REVERT: A 547 HIS cc_start: 0.6801 (t70) cc_final: 0.6549 (t70) REVERT: A 605 MET cc_start: 0.6951 (pmm) cc_final: 0.5869 (pmm) REVERT: A 657 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4283 (tpt) REVERT: A 677 LYS cc_start: 0.8750 (tmtt) cc_final: 0.8490 (tptt) REVERT: B 193 PHE cc_start: 0.8637 (m-10) cc_final: 0.8403 (m-80) REVERT: K -3 LEU cc_start: 0.7207 (pp) cc_final: 0.6864 (mp) outliers start: 49 outliers final: 38 residues processed: 299 average time/residue: 0.3812 time to fit residues: 186.2325 Evaluate side-chains 302 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 581 GLN Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26985 Z= 0.220 Angle : 0.551 12.889 36473 Z= 0.280 Chirality : 0.040 0.228 4105 Planarity : 0.003 0.049 4685 Dihedral : 4.054 67.706 3584 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.58 % Allowed : 14.18 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3269 helix: 1.09 (0.12), residues: 1978 sheet: -1.17 (0.55), residues: 90 loop : -1.08 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.006 0.001 HIS C 88 PHE 0.027 0.001 PHE D 193 TYR 0.024 0.001 TYR D 472 ARG 0.008 0.000 ARG L -5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 265 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8905 (tpp) cc_final: 0.8257 (tpt) REVERT: C 365 MET cc_start: 0.8539 (mmt) cc_final: 0.8251 (mmt) REVERT: C 451 MET cc_start: 0.8210 (mmp) cc_final: 0.7876 (mmp) REVERT: C 480 MET cc_start: 0.8149 (mmm) cc_final: 0.7766 (mmm) REVERT: C 538 GLN cc_start: 0.8144 (tp40) cc_final: 0.7436 (pp30) REVERT: F 91 GLU cc_start: 0.6924 (tp30) cc_final: 0.6703 (tp30) REVERT: G 17 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6559 (ttm) REVERT: A 236 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7227 (mpp) REVERT: A 547 HIS cc_start: 0.6843 (t70) cc_final: 0.6578 (t70) REVERT: A 605 MET cc_start: 0.6988 (pmm) cc_final: 0.5881 (pmm) REVERT: A 657 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4295 (tpt) REVERT: A 677 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8508 (tptt) REVERT: B 193 PHE cc_start: 0.8637 (m-10) cc_final: 0.8398 (m-80) REVERT: K -3 LEU cc_start: 0.7319 (pp) cc_final: 0.7001 (mp) outliers start: 46 outliers final: 42 residues processed: 286 average time/residue: 0.3693 time to fit residues: 173.4739 Evaluate side-chains 307 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 262 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 544 TYR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain D residue 367 TRP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 40 ASP Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 627 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.6980 chunk 273 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 237 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 581 GLN ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 HIS ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** 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 = 0.4309 r_free = 0.4309 target = 0.170164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133609 restraints weight = 44465.343| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.89 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26985 Z= 0.190 Angle : 0.542 13.200 36473 Z= 0.274 Chirality : 0.039 0.229 4105 Planarity : 0.003 0.049 4685 Dihedral : 4.051 68.407 3584 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.61 % Allowed : 14.35 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3269 helix: 1.13 (0.12), residues: 1966 sheet: -1.18 (0.55), residues: 90 loop : -1.07 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 367 HIS 0.005 0.001 HIS B 565 PHE 0.024 0.001 PHE D 193 TYR 0.021 0.001 TYR D 472 ARG 0.008 0.000 ARG L -5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5160.60 seconds wall clock time: 97 minutes 7.81 seconds (5827.81 seconds total)