Starting phenix.real_space_refine on Sat Feb 24 09:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/02_2024/7y53_33611_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/02_2024/7y53_33611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/02_2024/7y53_33611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/02_2024/7y53_33611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/02_2024/7y53_33611_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/02_2024/7y53_33611_updated.pdb" } resolution = 3.61 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= 0.004 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 230 5.16 5 C 27256 2.51 5 N 7466 2.21 5 O 7990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "C GLU 721": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42966 Number of models: 1 Model: "" Number of chains: 16 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "X" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Y" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Z" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "A" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "C" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5809 Classifications: {'peptide': 741} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain: "D" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5829 Classifications: {'peptide': 743} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain: "E" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5911 Classifications: {'peptide': 753} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 710} Chain: "F" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5921 Classifications: {'peptide': 755} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 712} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.68, per 1000 atoms: 0.50 Number of scatterers: 42966 At special positions: 0 Unit cell: (178.2, 166.1, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 24 15.00 O 7990 8.00 N 7466 7.00 C 27256 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.69 Conformation dependent library (CDL) restraints added in 7.6 seconds 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 243 helices and 31 sheets defined 44.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.58 Creating SS restraints... Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 13 through 31 Proline residue: W 26 - end of helix Processing helix chain 'W' and resid 36 through 38 No H-bonds generated for 'chain 'W' and resid 36 through 38' Processing helix chain 'W' and resid 43 through 48 Processing helix chain 'W' and resid 57 through 59 No H-bonds generated for 'chain 'W' and resid 57 through 59' Processing helix chain 'W' and resid 69 through 88 removed outlier: 4.145A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 115 Processing helix chain 'W' and resid 123 through 136 Processing helix chain 'W' and resid 155 through 165 Processing helix chain 'W' and resid 170 through 187 Processing helix chain 'W' and resid 189 through 193 Processing helix chain 'W' and resid 204 through 209 Processing helix chain 'X' and resid 3 through 10 Processing helix chain 'X' and resid 13 through 31 Proline residue: X 26 - end of helix Processing helix chain 'X' and resid 36 through 38 No H-bonds generated for 'chain 'X' and resid 36 through 38' Processing helix chain 'X' and resid 43 through 48 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 57 through 60 Processing helix chain 'X' and resid 69 through 88 removed outlier: 4.028A pdb=" N THR X 84 " --> pdb=" O TYR X 80 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG X 85 " --> pdb=" O GLN X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 115 Processing helix chain 'X' and resid 123 through 136 Processing helix chain 'X' and resid 155 through 165 Processing helix chain 'X' and resid 170 through 187 Processing helix chain 'X' and resid 189 through 193 Processing helix chain 'X' and resid 204 through 209 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 13 through 30 Proline residue: Y 26 - end of helix Processing helix chain 'Y' and resid 36 through 38 No H-bonds generated for 'chain 'Y' and resid 36 through 38' Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 52 through 59 removed outlier: 4.400A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 87 removed outlier: 4.467A pdb=" N THR Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Y 86 " --> pdb=" O TYR Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 115 Processing helix chain 'Y' and resid 123 through 136 Processing helix chain 'Y' and resid 155 through 165 removed outlier: 3.611A pdb=" N ILE Y 165 " --> pdb=" O GLY Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 170 through 187 removed outlier: 4.211A pdb=" N LEU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL Y 179 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY Y 180 " --> pdb=" O GLY Y 176 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 193 Processing helix chain 'Z' and resid 3 through 10 Processing helix chain 'Z' and resid 13 through 31 removed outlier: 3.590A pdb=" N ALA Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Z 21 " --> pdb=" O TYR Z 17 " (cutoff:3.500A) Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 43 through 48 Processing helix chain 'Z' and resid 53 through 60 removed outlier: 3.689A pdb=" N THR Z 59 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE Z 60 " --> pdb=" O ILE Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 88 removed outlier: 3.865A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 115 Processing helix chain 'Z' and resid 122 through 136 Processing helix chain 'Z' and resid 155 through 165 Processing helix chain 'Z' and resid 171 through 187 removed outlier: 3.897A pdb=" N GLY Z 176 " --> pdb=" O ASN Z 172 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Z 179 " --> pdb=" O ILE Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 193 No H-bonds generated for 'chain 'Z' and resid 190 through 193' Processing helix chain 'Z' and resid 204 through 209 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.577A pdb=" N SER A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 355 through 358 removed outlier: 3.501A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.707A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.787A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 594 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.813A pdb=" N VAL A 654 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 712 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.559A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.583A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.809A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.636A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.042A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.053A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 585 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 609 Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.556A pdb=" N ASN B 660 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 removed outlier: 3.631A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 764 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 210 through 225 removed outlier: 5.257A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.969A pdb=" N SER C 282 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 320 through 335 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.697A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 483 through 498 removed outlier: 4.005A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 removed outlier: 3.865A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 585 removed outlier: 4.177A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 584 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C 585 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 4.554A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 684 through 715 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 749 through 762 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 5.031A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 426 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.932A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.977A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.727A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 651 through 661 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 684 through 715 Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 210 through 225 removed outlier: 5.134A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 through 294 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.712A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 535 Processing helix chain 'E' and resid 544 through 551 Processing helix chain 'E' and resid 557 through 559 No H-bonds generated for 'chain 'E' and resid 557 through 559' Processing helix chain 'E' and resid 561 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 3.928A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 585 " --> pdb=" O ILE E 582 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG E 586 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 609 removed outlier: 4.275A pdb=" N GLY E 595 " --> pdb=" O ASP E 592 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 596 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 607 " --> pdb=" O ILE E 604 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP E 609 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 653 through 661 Processing helix chain 'E' and resid 674 through 678 Processing helix chain 'E' and resid 684 through 715 removed outlier: 5.653A pdb=" N THR E 715 " --> pdb=" O ARG E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 737 Processing helix chain 'E' and resid 749 through 765 removed outlier: 3.845A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.726A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.649A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 295 removed outlier: 4.157A pdb=" N GLU F 283 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU F 294 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'F' and resid 375 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.725A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.664A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 594 through 609 Processing helix chain 'F' and resid 650 through 662 removed outlier: 3.831A pdb=" N VAL F 654 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 661 " --> pdb=" O LYS F 658 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 662 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 764 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 30 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 removed outlier: 8.346A pdb=" N VAL A 39 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.914A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.547A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.559A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.280A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 645 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 81 through 83 removed outlier: 8.091A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= I, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.778A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.777A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.107A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.592A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.765A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'C' and resid 365 through 368 removed outlier: 6.625A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.428A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 645 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR C 517 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= R, first strand: chain 'D' and resid 38 through 41 removed outlier: 8.213A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.785A pdb=" N ARG D 113 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 365 through 368 removed outlier: 6.650A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.984A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 81 through 83 removed outlier: 8.503A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 151 through 155 Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.935A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.073A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.873A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= AB, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.911A pdb=" N ARG F 113 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AD, first strand: chain 'F' and resid 365 through 368 removed outlier: 6.743A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.710A pdb=" N ILE F 540 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP F 640 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) 1549 hydrogen bonds defined for protein. 4284 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: 15.31 Time building geometry restraints manager: 17.85 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: 14347 1.34 - 1.46: 9294 1.46 - 1.59: 19795 1.59 - 1.71: 36 1.71 - 1.83: 380 Bond restraints: 43852 Sorted by residual: bond pdb=" C VAL C 728 " pdb=" N PRO C 729 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.08e-02 8.57e+03 1.19e+01 bond pdb=" C SER F 664 " pdb=" N PRO F 665 " ideal model delta sigma weight residual 1.326 1.359 -0.032 1.44e-02 4.82e+03 5.04e+00 bond pdb=" CA ASP F 725 " pdb=" CB ASP F 725 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.33e-02 5.65e+03 3.38e+00 bond pdb=" C TYR E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.14e+00 bond pdb=" CA GLU B 34 " pdb=" CB GLU B 34 " ideal model delta sigma weight residual 1.518 1.547 -0.029 2.08e-02 2.31e+03 1.98e+00 ... (remaining 43847 not shown) Histogram of bond angle deviations from ideal: 97.30 - 105.05: 1048 105.05 - 112.80: 23110 112.80 - 120.55: 19148 120.55 - 128.30: 15810 128.30 - 136.05: 276 Bond angle restraints: 59392 Sorted by residual: angle pdb=" N VAL E 559 " pdb=" CA VAL E 559 " pdb=" C VAL E 559 " ideal model delta sigma weight residual 112.90 107.84 5.06 9.60e-01 1.09e+00 2.77e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 113.71 109.27 4.44 9.50e-01 1.11e+00 2.18e+01 angle pdb=" CB ARG F 713 " pdb=" CG ARG F 713 " pdb=" CD ARG F 713 " ideal model delta sigma weight residual 111.30 121.97 -10.67 2.30e+00 1.89e-01 2.15e+01 angle pdb=" C LEU B 492 " pdb=" N VAL B 493 " pdb=" CA VAL B 493 " ideal model delta sigma weight residual 122.77 117.97 4.80 1.05e+00 9.07e-01 2.09e+01 angle pdb=" C GLU B 34 " pdb=" CA GLU B 34 " pdb=" CB GLU B 34 " ideal model delta sigma weight residual 115.79 110.43 5.36 1.19e+00 7.06e-01 2.03e+01 ... (remaining 59387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 26153 35.04 - 70.08: 473 70.08 - 105.12: 68 105.12 - 140.15: 19 140.15 - 175.19: 2 Dihedral angle restraints: 26715 sinusoidal: 11199 harmonic: 15516 Sorted by residual: dihedral pdb=" CA ASP F 726 " pdb=" C ASP F 726 " pdb=" N PRO F 727 " pdb=" CA PRO F 727 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 124.80 175.19 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 148.45 151.55 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 26712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5236 0.055 - 0.111: 1151 0.111 - 0.166: 169 0.166 - 0.221: 10 0.221 - 0.276: 1 Chirality restraints: 6567 Sorted by residual: chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA MET D 427 " pdb=" N MET D 427 " pdb=" C MET D 427 " pdb=" CB MET D 427 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG D 711 " pdb=" N ARG D 711 " pdb=" C ARG D 711 " pdb=" CB ARG D 711 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 6564 not shown) Planarity restraints: 7737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 726 " -0.081 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO F 727 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 727 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 727 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 551 " 0.023 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" CG TRP C 551 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 551 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 551 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 551 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 551 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 551 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 551 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 551 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 551 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 297 " 0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO F 298 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.051 5.00e-02 4.00e+02 ... (remaining 7734 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 781 2.68 - 3.23: 42535 3.23 - 3.79: 64904 3.79 - 4.34: 82395 4.34 - 4.90: 133258 Nonbonded interactions: 323873 Sorted by model distance: nonbonded pdb=" OG1 THR Y 202 " pdb=" OH TYR Y 207 " model vdw 2.119 2.440 nonbonded pdb=" O ASN C 624 " pdb=" OH TYR C 755 " model vdw 2.123 2.440 nonbonded pdb=" O ASN B 624 " pdb=" OH TYR B 755 " model vdw 2.139 2.440 nonbonded pdb=" OG SER D 664 " pdb=" O LYS F 505 " model vdw 2.156 2.440 nonbonded pdb=" NH2 ARG E 653 " pdb=" O THR E 679 " model vdw 2.173 2.520 ... (remaining 323868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'B' and (resid 23 through 763 or resid 901 through 902)) selection = chain 'C' selection = (chain 'D' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'E' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'F' and (resid 23 through 763 or resid 901 through 902)) } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.730 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 107.180 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.270 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 43852 Z= 0.239 Angle : 0.709 10.669 59392 Z= 0.367 Chirality : 0.046 0.276 6567 Planarity : 0.005 0.125 7737 Dihedral : 15.238 175.193 16697 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.63 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.33 (0.12), residues: 5362 helix: 0.89 (0.11), residues: 2374 sheet: 0.21 (0.21), residues: 691 loop : -1.55 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP C 551 HIS 0.010 0.001 HIS E 499 PHE 0.045 0.001 PHE C 552 TYR 0.029 0.001 TYR C 755 ARG 0.018 0.001 ARG D 711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 5.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 82 TYR cc_start: 0.8089 (m-80) cc_final: 0.7681 (m-80) REVERT: W 106 TRP cc_start: 0.7038 (t60) cc_final: 0.6793 (t60) REVERT: X 57 THR cc_start: 0.6454 (p) cc_final: 0.6215 (p) REVERT: Y 116 MET cc_start: 0.5638 (mmp) cc_final: 0.5239 (mmm) REVERT: Y 192 MET cc_start: 0.6109 (ptt) cc_final: 0.5828 (ptt) REVERT: Z 127 MET cc_start: 0.8995 (pmm) cc_final: 0.8148 (pmm) REVERT: Z 163 ASN cc_start: 0.8419 (t0) cc_final: 0.8192 (p0) REVERT: Z 173 GLU cc_start: 0.8623 (mp0) cc_final: 0.8108 (mp0) REVERT: Z 198 ASN cc_start: 0.8092 (t0) cc_final: 0.7845 (t0) REVERT: B 561 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 244 TYR cc_start: 0.7932 (p90) cc_final: 0.7661 (p90) REVERT: C 531 ILE cc_start: 0.9238 (tp) cc_final: 0.9033 (tp) REVERT: D 720 MET cc_start: 0.0445 (mtp) cc_final: 0.0175 (mtm) REVERT: E 46 MET cc_start: 0.6860 (mtp) cc_final: 0.5230 (tpt) REVERT: E 244 TYR cc_start: 0.7468 (p90) cc_final: 0.6806 (p90) REVERT: E 561 GLU cc_start: 0.7574 (pm20) cc_final: 0.7273 (pm20) REVERT: F 244 TYR cc_start: 0.7827 (p90) cc_final: 0.7583 (p90) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.5281 time to fit residues: 396.0448 Evaluate side-chains 330 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 5.9990 chunk 404 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 418 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 311 optimal weight: 6.9990 chunk 484 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 181 HIS ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 499 HIS ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43852 Z= 0.192 Angle : 0.640 10.150 59392 Z= 0.310 Chirality : 0.045 0.204 6567 Planarity : 0.005 0.096 7737 Dihedral : 9.275 166.978 6027 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.96 % Favored : 91.64 % Rotamer: Outliers : 0.72 % Allowed : 7.51 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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 (0.12), residues: 5362 helix: 0.93 (0.11), residues: 2381 sheet: 0.22 (0.20), residues: 696 loop : -1.55 (0.14), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 551 HIS 0.006 0.001 HIS F 404 PHE 0.018 0.001 PHE B 360 TYR 0.039 0.001 TYR D 495 ARG 0.007 0.000 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 364 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 38 TYR cc_start: 0.3578 (OUTLIER) cc_final: 0.2277 (t80) REVERT: W 82 TYR cc_start: 0.7942 (m-80) cc_final: 0.7354 (m-80) REVERT: W 106 TRP cc_start: 0.7026 (t60) cc_final: 0.6763 (t60) REVERT: X 57 THR cc_start: 0.6300 (p) cc_final: 0.6099 (p) REVERT: X 192 MET cc_start: 0.8973 (ppp) cc_final: 0.8668 (ppp) REVERT: Z 1 MET cc_start: 0.4075 (ttt) cc_final: 0.3422 (tmm) REVERT: Z 163 ASN cc_start: 0.8533 (t0) cc_final: 0.8264 (p0) REVERT: Z 173 GLU cc_start: 0.8979 (mp0) cc_final: 0.8327 (mp0) REVERT: Z 192 MET cc_start: 0.7598 (ptt) cc_final: 0.7333 (ptp) REVERT: Z 198 ASN cc_start: 0.8156 (t0) cc_final: 0.7952 (t0) REVERT: B 508 MET cc_start: 0.2885 (mmm) cc_final: 0.2664 (mmm) REVERT: B 561 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 173 TYR cc_start: 0.6508 (p90) cc_final: 0.6154 (p90) REVERT: C 244 TYR cc_start: 0.7920 (p90) cc_final: 0.7653 (p90) REVERT: C 531 ILE cc_start: 0.9241 (tp) cc_final: 0.9016 (tp) REVERT: C 702 SER cc_start: 0.8725 (t) cc_final: 0.8231 (p) REVERT: D 205 ASP cc_start: 0.8586 (t0) cc_final: 0.8194 (t70) REVERT: D 508 MET cc_start: 0.3940 (OUTLIER) cc_final: 0.2413 (tmm) REVERT: D 582 ILE cc_start: 0.7201 (mm) cc_final: 0.6960 (mm) REVERT: D 720 MET cc_start: 0.0439 (mtp) cc_final: 0.0164 (mtm) REVERT: E 46 MET cc_start: 0.6862 (mtp) cc_final: 0.5350 (tpt) REVERT: E 84 MET cc_start: 0.6482 (ppp) cc_final: 0.6173 (ppp) REVERT: E 244 TYR cc_start: 0.7805 (p90) cc_final: 0.7575 (p90) REVERT: E 315 LYS cc_start: 0.8589 (tppt) cc_final: 0.8293 (tptt) REVERT: E 427 MET cc_start: 0.8533 (tmm) cc_final: 0.8300 (tmm) REVERT: E 608 MET cc_start: 0.8625 (tmm) cc_final: 0.8319 (tmm) REVERT: F 740 MET cc_start: 0.8662 (tmm) cc_final: 0.8397 (tmm) outliers start: 33 outliers final: 18 residues processed: 378 average time/residue: 0.5345 time to fit residues: 341.9443 Evaluate side-chains 353 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 333 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 8.9990 chunk 150 optimal weight: 0.0980 chunk 403 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 485 optimal weight: 0.9990 chunk 524 optimal weight: 1.9990 chunk 432 optimal weight: 9.9990 chunk 481 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 389 optimal weight: 20.0000 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43852 Z= 0.197 Angle : 0.619 9.412 59392 Z= 0.298 Chirality : 0.044 0.191 6567 Planarity : 0.005 0.094 7737 Dihedral : 8.969 152.490 6027 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.21 % Favored : 91.40 % Rotamer: Outliers : 0.94 % Allowed : 10.36 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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 (0.12), residues: 5362 helix: 0.94 (0.11), residues: 2380 sheet: 0.18 (0.20), residues: 697 loop : -1.52 (0.14), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 551 HIS 0.003 0.001 HIS E 404 PHE 0.017 0.001 PHE D 552 TYR 0.024 0.001 TYR D 495 ARG 0.006 0.000 ARG X 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 348 time to evaluate : 5.019 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: W 38 TYR cc_start: 0.3355 (OUTLIER) cc_final: 0.2443 (t80) REVERT: W 106 TRP cc_start: 0.7004 (t60) cc_final: 0.6746 (t60) REVERT: W 182 LEU cc_start: 0.9252 (mm) cc_final: 0.8906 (pp) REVERT: X 57 THR cc_start: 0.6385 (p) cc_final: 0.6160 (p) REVERT: X 192 MET cc_start: 0.9000 (ppp) cc_final: 0.8642 (ppp) REVERT: Y 172 ASN cc_start: 0.8321 (m-40) cc_final: 0.7812 (p0) REVERT: Y 187 MET cc_start: 0.8605 (tpp) cc_final: 0.8352 (tpp) REVERT: Z 1 MET cc_start: 0.4019 (ttt) cc_final: 0.3397 (tmm) REVERT: Z 163 ASN cc_start: 0.8556 (t0) cc_final: 0.8260 (p0) REVERT: Z 173 GLU cc_start: 0.8903 (mp0) cc_final: 0.8307 (mp0) REVERT: Z 192 MET cc_start: 0.7604 (ptt) cc_final: 0.7284 (ptp) REVERT: B 561 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 173 TYR cc_start: 0.6568 (p90) cc_final: 0.6208 (p90) REVERT: C 244 TYR cc_start: 0.7899 (p90) cc_final: 0.7645 (p90) REVERT: C 531 ILE cc_start: 0.9239 (tp) cc_final: 0.9005 (tp) REVERT: C 702 SER cc_start: 0.8824 (t) cc_final: 0.8294 (p) REVERT: D 205 ASP cc_start: 0.8563 (t0) cc_final: 0.8167 (t70) REVERT: D 508 MET cc_start: 0.4087 (OUTLIER) cc_final: 0.2499 (tmm) REVERT: D 678 MET cc_start: 0.8106 (tpp) cc_final: 0.7880 (tpp) REVERT: E 46 MET cc_start: 0.6829 (mtp) cc_final: 0.5201 (tpt) REVERT: E 244 TYR cc_start: 0.7740 (p90) cc_final: 0.7502 (p90) REVERT: E 427 MET cc_start: 0.8537 (tmm) cc_final: 0.8266 (tmm) REVERT: F 607 GLU cc_start: 0.8084 (mp0) cc_final: 0.7811 (mp0) REVERT: F 740 MET cc_start: 0.8634 (tmm) cc_final: 0.8351 (tmm) outliers start: 43 outliers final: 29 residues processed: 368 average time/residue: 0.5173 time to fit residues: 323.8679 Evaluate side-chains 358 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 4.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 231 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 487 optimal weight: 0.4980 chunk 516 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 462 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 HIS D 317 HIS D 538 ASN D 602 ASN D 603 GLN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43852 Z= 0.209 Angle : 0.623 12.039 59392 Z= 0.298 Chirality : 0.044 0.195 6567 Planarity : 0.005 0.093 7737 Dihedral : 8.797 149.329 6027 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.96 % Favored : 91.64 % Rotamer: Outliers : 1.28 % Allowed : 12.19 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5362 helix: 0.94 (0.11), residues: 2387 sheet: 0.08 (0.20), residues: 705 loop : -1.55 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 551 HIS 0.021 0.001 HIS A 499 PHE 0.028 0.001 PHE B 575 TYR 0.022 0.001 TYR F 244 ARG 0.004 0.000 ARG X 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 5.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 78 PHE cc_start: 0.8991 (m-80) cc_final: 0.8739 (m-80) REVERT: W 82 TYR cc_start: 0.7885 (m-80) cc_final: 0.7404 (m-80) REVERT: W 106 TRP cc_start: 0.7031 (t60) cc_final: 0.6772 (t60) REVERT: X 57 THR cc_start: 0.6459 (p) cc_final: 0.6227 (p) REVERT: X 192 MET cc_start: 0.8993 (ppp) cc_final: 0.8649 (ppp) REVERT: Y 172 ASN cc_start: 0.8338 (m-40) cc_final: 0.7812 (p0) REVERT: Y 187 MET cc_start: 0.8550 (tpp) cc_final: 0.8345 (tpp) REVERT: Y 204 GLN cc_start: 0.8313 (tp-100) cc_final: 0.8098 (tm-30) REVERT: Z 1 MET cc_start: 0.4364 (ttt) cc_final: 0.3639 (tmm) REVERT: Z 127 MET cc_start: 0.8988 (pmm) cc_final: 0.8391 (ppp) REVERT: Z 163 ASN cc_start: 0.8578 (t0) cc_final: 0.8323 (p0) REVERT: Z 173 GLU cc_start: 0.8876 (mp0) cc_final: 0.7814 (mp0) REVERT: Z 192 MET cc_start: 0.7688 (ptt) cc_final: 0.7424 (ptp) REVERT: B 561 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7595 (tm-30) REVERT: C 173 TYR cc_start: 0.6608 (p90) cc_final: 0.6226 (p90) REVERT: C 244 TYR cc_start: 0.7866 (p90) cc_final: 0.7606 (p90) REVERT: C 702 SER cc_start: 0.8846 (t) cc_final: 0.8312 (p) REVERT: D 205 ASP cc_start: 0.8577 (t0) cc_final: 0.8182 (t70) REVERT: D 508 MET cc_start: 0.4400 (OUTLIER) cc_final: 0.4108 (ttm) REVERT: D 678 MET cc_start: 0.8119 (tpp) cc_final: 0.7886 (tpp) REVERT: D 720 MET cc_start: 0.0198 (OUTLIER) cc_final: -0.0141 (mtp) REVERT: D 730 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4587 (pm20) REVERT: E 46 MET cc_start: 0.6744 (mtp) cc_final: 0.5292 (tpt) REVERT: E 244 TYR cc_start: 0.7772 (p90) cc_final: 0.7540 (p90) REVERT: E 379 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: E 427 MET cc_start: 0.8547 (tmm) cc_final: 0.8265 (tmm) REVERT: E 607 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: E 608 MET cc_start: 0.8639 (tmm) cc_final: 0.8231 (tmm) REVERT: F 491 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7809 (mm-30) REVERT: F 607 GLU cc_start: 0.8227 (mp0) cc_final: 0.7930 (mp0) REVERT: F 740 MET cc_start: 0.8738 (tmm) cc_final: 0.8460 (tmm) outliers start: 59 outliers final: 35 residues processed: 369 average time/residue: 0.5185 time to fit residues: 324.5943 Evaluate side-chains 362 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 322 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 607 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 384 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 440 optimal weight: 0.0870 chunk 356 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 263 optimal weight: 1.9990 chunk 463 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 602 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43852 Z= 0.264 Angle : 0.648 13.704 59392 Z= 0.310 Chirality : 0.045 0.196 6567 Planarity : 0.005 0.092 7737 Dihedral : 8.682 154.555 6027 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.39 % Favored : 91.23 % Rotamer: Outliers : 1.37 % Allowed : 14.36 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.39 (0.12), residues: 5362 helix: 0.87 (0.11), residues: 2386 sheet: -0.03 (0.20), residues: 708 loop : -1.58 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 551 HIS 0.015 0.001 HIS A 499 PHE 0.018 0.001 PHE B 575 TYR 0.022 0.001 TYR F 244 ARG 0.005 0.000 ARG X 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 334 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 82 TYR cc_start: 0.7956 (m-80) cc_final: 0.7609 (m-80) REVERT: W 106 TRP cc_start: 0.7171 (t60) cc_final: 0.6818 (t60) REVERT: X 57 THR cc_start: 0.6576 (p) cc_final: 0.6331 (p) REVERT: X 122 MET cc_start: 0.7978 (tmt) cc_final: 0.7710 (tmt) REVERT: X 192 MET cc_start: 0.8977 (ppp) cc_final: 0.8630 (ppp) REVERT: Y 172 ASN cc_start: 0.8358 (m110) cc_final: 0.7870 (p0) REVERT: Y 187 MET cc_start: 0.8568 (tpp) cc_final: 0.8361 (tpp) REVERT: Z 1 MET cc_start: 0.4335 (ttt) cc_final: 0.3780 (tmm) REVERT: Z 127 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8436 (ppp) REVERT: Z 163 ASN cc_start: 0.8494 (t0) cc_final: 0.8291 (p0) REVERT: Z 173 GLU cc_start: 0.8899 (mp0) cc_final: 0.7866 (mp0) REVERT: Z 192 MET cc_start: 0.7544 (ptt) cc_final: 0.7220 (ptp) REVERT: A 286 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8753 (tt) REVERT: B 561 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 173 TYR cc_start: 0.6760 (p90) cc_final: 0.6363 (p90) REVERT: C 244 TYR cc_start: 0.7882 (p90) cc_final: 0.7623 (p90) REVERT: D 508 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4303 (ttm) REVERT: D 720 MET cc_start: 0.0260 (OUTLIER) cc_final: -0.0059 (mtp) REVERT: D 730 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4723 (pm20) REVERT: E 244 TYR cc_start: 0.7831 (p90) cc_final: 0.7591 (p90) REVERT: E 315 LYS cc_start: 0.8639 (tppt) cc_final: 0.8210 (tptt) REVERT: E 379 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: E 427 MET cc_start: 0.8587 (tmm) cc_final: 0.8232 (tmm) REVERT: E 607 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: F 740 MET cc_start: 0.8630 (tmm) cc_final: 0.8305 (tmm) outliers start: 63 outliers final: 41 residues processed: 373 average time/residue: 0.5551 time to fit residues: 346.4440 Evaluate side-chains 363 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 315 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Y residue 208 ARG Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 607 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 0.6980 chunk 464 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 516 optimal weight: 5.9990 chunk 428 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 135 GLN ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 602 ASN D 714 GLN E 602 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 43852 Z= 0.157 Angle : 0.617 11.760 59392 Z= 0.292 Chirality : 0.043 0.212 6567 Planarity : 0.004 0.087 7737 Dihedral : 8.335 154.919 6027 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.65 % Favored : 92.02 % Rotamer: Outliers : 1.44 % Allowed : 15.47 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.25 (0.12), residues: 5362 helix: 1.00 (0.11), residues: 2382 sheet: 0.10 (0.20), residues: 700 loop : -1.54 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 551 HIS 0.006 0.001 HIS A 499 PHE 0.022 0.001 PHE W 78 TYR 0.024 0.001 TYR F 244 ARG 0.004 0.000 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 355 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 78 PHE cc_start: 0.8951 (m-80) cc_final: 0.8682 (m-80) REVERT: W 106 TRP cc_start: 0.7022 (t60) cc_final: 0.6701 (t60) REVERT: X 122 MET cc_start: 0.7973 (tmt) cc_final: 0.7556 (tmm) REVERT: X 192 MET cc_start: 0.8976 (ppp) cc_final: 0.8599 (ppp) REVERT: Y 172 ASN cc_start: 0.8351 (m110) cc_final: 0.7897 (p0) REVERT: Z 1 MET cc_start: 0.4379 (ttt) cc_final: 0.3842 (tmm) REVERT: Z 127 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8379 (ppp) REVERT: Z 163 ASN cc_start: 0.8418 (t0) cc_final: 0.8181 (p0) REVERT: Z 173 GLU cc_start: 0.8909 (mp0) cc_final: 0.7888 (mp0) REVERT: Z 192 MET cc_start: 0.7382 (ptt) cc_final: 0.7135 (ptt) REVERT: B 180 THR cc_start: 0.7091 (OUTLIER) cc_final: 0.6688 (p) REVERT: B 561 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 173 TYR cc_start: 0.6661 (p90) cc_final: 0.6211 (p90) REVERT: C 244 TYR cc_start: 0.7776 (p90) cc_final: 0.7530 (p90) REVERT: C 702 SER cc_start: 0.8898 (t) cc_final: 0.8371 (p) REVERT: D 205 ASP cc_start: 0.8512 (t0) cc_final: 0.8182 (t70) REVERT: D 508 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.2888 (tmm) REVERT: D 602 ASN cc_start: 0.8297 (m-40) cc_final: 0.8034 (m-40) REVERT: D 678 MET cc_start: 0.8048 (tpp) cc_final: 0.7807 (tpp) REVERT: D 720 MET cc_start: 0.0247 (OUTLIER) cc_final: -0.0059 (mtp) REVERT: D 730 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.4869 (pm20) REVERT: E 244 TYR cc_start: 0.7821 (p90) cc_final: 0.7620 (p90) REVERT: E 315 LYS cc_start: 0.8607 (tppt) cc_final: 0.8161 (tptt) REVERT: E 379 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: E 427 MET cc_start: 0.8549 (tmm) cc_final: 0.8192 (tmm) REVERT: F 607 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: F 608 MET cc_start: 0.7985 (mtm) cc_final: 0.7632 (mtm) REVERT: F 740 MET cc_start: 0.8595 (tmm) cc_final: 0.8270 (tmm) outliers start: 66 outliers final: 35 residues processed: 396 average time/residue: 0.5248 time to fit residues: 349.9331 Evaluate side-chains 373 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 331 time to evaluate : 5.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Y residue 208 ARG Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 292 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 514 optimal weight: 5.9990 chunk 322 optimal weight: 0.0870 chunk 313 optimal weight: 8.9990 chunk 237 optimal weight: 0.6980 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS F 404 HIS F 714 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43852 Z= 0.205 Angle : 0.632 14.688 59392 Z= 0.299 Chirality : 0.044 0.204 6567 Planarity : 0.004 0.086 7737 Dihedral : 8.228 156.443 6027 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.00 % Favored : 91.66 % Rotamer: Outliers : 1.31 % Allowed : 15.97 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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 (0.12), residues: 5362 helix: 1.00 (0.11), residues: 2380 sheet: 0.04 (0.20), residues: 699 loop : -1.53 (0.14), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 551 HIS 0.007 0.001 HIS F 404 PHE 0.016 0.001 PHE B 360 TYR 0.023 0.001 TYR F 244 ARG 0.005 0.000 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 336 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 78 PHE cc_start: 0.9050 (m-80) cc_final: 0.8658 (m-80) REVERT: W 106 TRP cc_start: 0.7054 (t60) cc_final: 0.6725 (t60) REVERT: X 122 MET cc_start: 0.8032 (tmt) cc_final: 0.7752 (tmt) REVERT: X 192 MET cc_start: 0.8993 (ppp) cc_final: 0.8606 (ppp) REVERT: Y 172 ASN cc_start: 0.8352 (m110) cc_final: 0.7904 (p0) REVERT: Z 1 MET cc_start: 0.4474 (ttt) cc_final: 0.3941 (tmm) REVERT: Z 127 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8398 (ppp) REVERT: Z 173 GLU cc_start: 0.8903 (mp0) cc_final: 0.7846 (mp0) REVERT: A 286 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 561 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 173 TYR cc_start: 0.6718 (p90) cc_final: 0.6255 (p90) REVERT: C 244 TYR cc_start: 0.7858 (p90) cc_final: 0.7575 (p90) REVERT: C 702 SER cc_start: 0.8920 (t) cc_final: 0.8383 (p) REVERT: C 744 ARG cc_start: 0.5375 (mmt-90) cc_final: 0.5026 (mmt-90) REVERT: D 205 ASP cc_start: 0.8526 (t0) cc_final: 0.8259 (t70) REVERT: D 508 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.4191 (ttm) REVERT: D 602 ASN cc_start: 0.8323 (m-40) cc_final: 0.8035 (m-40) REVERT: D 720 MET cc_start: 0.0694 (OUTLIER) cc_final: 0.0471 (mtp) REVERT: D 730 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.4840 (pm20) REVERT: E 46 MET cc_start: 0.6357 (ptp) cc_final: 0.4956 (tpt) REVERT: E 244 TYR cc_start: 0.7840 (p90) cc_final: 0.7631 (p90) REVERT: E 315 LYS cc_start: 0.8600 (tppt) cc_final: 0.8196 (tptt) REVERT: E 379 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: E 427 MET cc_start: 0.8564 (tmm) cc_final: 0.8250 (tmm) REVERT: F 607 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: F 740 MET cc_start: 0.8608 (tmm) cc_final: 0.8277 (tmm) outliers start: 60 outliers final: 39 residues processed: 371 average time/residue: 0.5048 time to fit residues: 319.7674 Evaluate side-chains 367 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 321 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 327 optimal weight: 0.1980 chunk 350 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 47 optimal weight: 40.0000 chunk 404 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 43852 Z= 0.153 Angle : 0.626 13.809 59392 Z= 0.293 Chirality : 0.043 0.224 6567 Planarity : 0.004 0.082 7737 Dihedral : 8.046 154.429 6027 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.35 % Favored : 92.33 % Rotamer: Outliers : 1.35 % Allowed : 16.34 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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 (0.12), residues: 5362 helix: 1.04 (0.11), residues: 2390 sheet: 0.17 (0.20), residues: 690 loop : -1.48 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP Y 42 HIS 0.003 0.000 HIS F 340 PHE 0.013 0.001 PHE D 552 TYR 0.025 0.001 TYR F 244 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 353 time to evaluate : 5.105 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: W 1 MET cc_start: 0.4006 (ttt) cc_final: 0.3348 (tmm) REVERT: W 78 PHE cc_start: 0.9107 (m-80) cc_final: 0.8735 (m-80) REVERT: W 106 TRP cc_start: 0.6990 (t60) cc_final: 0.6659 (t60) REVERT: X 122 MET cc_start: 0.8017 (tmt) cc_final: 0.7579 (tmm) REVERT: X 192 MET cc_start: 0.8993 (ppp) cc_final: 0.8600 (ppp) REVERT: Y 101 MET cc_start: 0.7934 (ppp) cc_final: 0.7230 (pmm) REVERT: Y 172 ASN cc_start: 0.8273 (m110) cc_final: 0.7867 (p0) REVERT: Z 1 MET cc_start: 0.4569 (ttt) cc_final: 0.4027 (tmm) REVERT: Z 127 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8401 (ppp) REVERT: Z 173 GLU cc_start: 0.8793 (mp0) cc_final: 0.7902 (mp0) REVERT: A 286 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 561 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 173 TYR cc_start: 0.6718 (p90) cc_final: 0.6237 (p90) REVERT: C 244 TYR cc_start: 0.7780 (p90) cc_final: 0.7510 (p90) REVERT: C 702 SER cc_start: 0.8864 (t) cc_final: 0.8332 (p) REVERT: C 744 ARG cc_start: 0.5439 (mmt-90) cc_final: 0.5128 (mmt-90) REVERT: D 205 ASP cc_start: 0.8437 (t0) cc_final: 0.8140 (t70) REVERT: D 508 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.2972 (tmm) REVERT: D 602 ASN cc_start: 0.8233 (m-40) cc_final: 0.7994 (m-40) REVERT: D 661 LEU cc_start: 0.8246 (tp) cc_final: 0.7678 (tt) REVERT: D 720 MET cc_start: 0.0663 (OUTLIER) cc_final: 0.0451 (mtp) REVERT: D 730 GLU cc_start: 0.5229 (OUTLIER) cc_final: 0.4946 (pm20) REVERT: E 315 LYS cc_start: 0.8533 (tppt) cc_final: 0.8145 (tptt) REVERT: E 379 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: E 427 MET cc_start: 0.8549 (tmm) cc_final: 0.8246 (tmm) REVERT: F 607 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: F 740 MET cc_start: 0.8581 (tmm) cc_final: 0.8263 (tmm) outliers start: 62 outliers final: 39 residues processed: 390 average time/residue: 0.5072 time to fit residues: 335.6294 Evaluate side-chains 386 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 340 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Y residue 208 ARG Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 139 ASP Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 2.9990 chunk 493 optimal weight: 3.9990 chunk 449 optimal weight: 0.4980 chunk 479 optimal weight: 1.9990 chunk 492 optimal weight: 0.6980 chunk 288 optimal weight: 0.0570 chunk 208 optimal weight: 0.0070 chunk 376 optimal weight: 6.9990 chunk 147 optimal weight: 0.0170 chunk 433 optimal weight: 0.6980 chunk 453 optimal weight: 0.1980 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 603 GLN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 43852 Z= 0.144 Angle : 0.626 12.219 59392 Z= 0.293 Chirality : 0.043 0.265 6567 Planarity : 0.004 0.078 7737 Dihedral : 7.809 151.318 6027 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.22 % Favored : 92.45 % Rotamer: Outliers : 0.96 % Allowed : 17.32 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.07 (0.12), residues: 5362 helix: 1.14 (0.11), residues: 2368 sheet: 0.27 (0.20), residues: 700 loop : -1.44 (0.14), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP Z 106 HIS 0.003 0.000 HIS F 340 PHE 0.051 0.001 PHE B 265 TYR 0.027 0.001 TYR F 244 ARG 0.004 0.000 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 376 time to evaluate : 5.192 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: W 1 MET cc_start: 0.4106 (ttt) cc_final: 0.3475 (tmm) REVERT: W 38 TYR cc_start: 0.3494 (OUTLIER) cc_final: 0.2593 (t80) REVERT: W 78 PHE cc_start: 0.9112 (m-80) cc_final: 0.8736 (m-80) REVERT: W 106 TRP cc_start: 0.6965 (t60) cc_final: 0.6658 (t60) REVERT: W 182 LEU cc_start: 0.9258 (mm) cc_final: 0.8922 (pp) REVERT: X 122 MET cc_start: 0.8010 (tmt) cc_final: 0.7562 (tmm) REVERT: X 192 MET cc_start: 0.8993 (ppp) cc_final: 0.8595 (ppp) REVERT: Y 172 ASN cc_start: 0.8280 (m110) cc_final: 0.7864 (p0) REVERT: Z 1 MET cc_start: 0.4398 (ttt) cc_final: 0.3889 (tmm) REVERT: Z 127 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8459 (ppp) REVERT: Z 157 TRP cc_start: 0.8563 (m100) cc_final: 0.8105 (m100) REVERT: Z 173 GLU cc_start: 0.8756 (mp0) cc_final: 0.8203 (mp0) REVERT: B 561 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 173 TYR cc_start: 0.6704 (p90) cc_final: 0.6213 (p90) REVERT: C 244 TYR cc_start: 0.7718 (p90) cc_final: 0.7440 (p90) REVERT: C 427 MET cc_start: 0.7849 (tpp) cc_final: 0.7583 (tpp) REVERT: C 531 ILE cc_start: 0.9197 (tp) cc_final: 0.8890 (tp) REVERT: C 702 SER cc_start: 0.8817 (t) cc_final: 0.8300 (p) REVERT: C 744 ARG cc_start: 0.5387 (mmt-90) cc_final: 0.5097 (mmt-90) REVERT: D 205 ASP cc_start: 0.8212 (t0) cc_final: 0.7939 (t70) REVERT: D 508 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.2978 (tmm) REVERT: D 651 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7422 (tttm) REVERT: E 379 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: E 427 MET cc_start: 0.8533 (tmm) cc_final: 0.8270 (tmm) REVERT: F 740 MET cc_start: 0.8561 (tmm) cc_final: 0.8246 (tmm) outliers start: 44 outliers final: 22 residues processed: 402 average time/residue: 0.5129 time to fit residues: 349.5786 Evaluate side-chains 368 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 341 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 0.2980 chunk 314 optimal weight: 9.9990 chunk 507 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 352 optimal weight: 0.1980 chunk 532 optimal weight: 4.9990 chunk 489 optimal weight: 0.6980 chunk 423 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 327 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 43852 Z= 0.152 Angle : 0.636 12.400 59392 Z= 0.297 Chirality : 0.043 0.226 6567 Planarity : 0.004 0.075 7737 Dihedral : 7.728 148.532 6027 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.96 % Favored : 92.71 % Rotamer: Outliers : 0.81 % Allowed : 17.63 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 5362 helix: 1.16 (0.11), residues: 2371 sheet: 0.38 (0.20), residues: 694 loop : -1.44 (0.14), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP Y 42 HIS 0.006 0.000 HIS F 404 PHE 0.043 0.001 PHE B 265 TYR 0.025 0.001 TYR F 244 ARG 0.005 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 350 time to evaluate : 5.455 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: W 1 MET cc_start: 0.4022 (ttt) cc_final: 0.3420 (tmm) REVERT: W 38 TYR cc_start: 0.3486 (OUTLIER) cc_final: 0.2622 (t80) REVERT: W 106 TRP cc_start: 0.6997 (t60) cc_final: 0.6670 (t60) REVERT: W 182 LEU cc_start: 0.9257 (mm) cc_final: 0.8927 (pp) REVERT: X 57 THR cc_start: 0.6480 (p) cc_final: 0.6250 (p) REVERT: X 122 MET cc_start: 0.7987 (tmt) cc_final: 0.7539 (tmm) REVERT: X 192 MET cc_start: 0.8996 (ppp) cc_final: 0.8597 (ppp) REVERT: Y 172 ASN cc_start: 0.8289 (m110) cc_final: 0.7863 (p0) REVERT: Y 192 MET cc_start: 0.6263 (ptt) cc_final: 0.5269 (ppp) REVERT: Z 1 MET cc_start: 0.4431 (ttt) cc_final: 0.3911 (tmm) REVERT: Z 127 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8402 (ppp) REVERT: Z 157 TRP cc_start: 0.8558 (m100) cc_final: 0.8084 (m100) REVERT: Z 173 GLU cc_start: 0.8753 (mp0) cc_final: 0.8198 (mp0) REVERT: B 561 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 173 TYR cc_start: 0.6722 (p90) cc_final: 0.6228 (p90) REVERT: C 244 TYR cc_start: 0.7712 (p90) cc_final: 0.7411 (p90) REVERT: C 427 MET cc_start: 0.7879 (tpp) cc_final: 0.7634 (tpp) REVERT: C 531 ILE cc_start: 0.9200 (tp) cc_final: 0.8893 (tp) REVERT: C 551 TRP cc_start: 0.8292 (t60) cc_final: 0.7983 (t60) REVERT: C 702 SER cc_start: 0.8825 (t) cc_final: 0.8301 (p) REVERT: C 744 ARG cc_start: 0.5406 (mmt-90) cc_final: 0.5114 (mmt-90) REVERT: D 508 MET cc_start: 0.4580 (OUTLIER) cc_final: 0.2992 (tmm) REVERT: D 651 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7434 (tttm) REVERT: D 720 MET cc_start: 0.1653 (mtp) cc_final: 0.1318 (ttt) REVERT: E 117 LEU cc_start: 0.7975 (mt) cc_final: 0.7683 (pp) REVERT: E 379 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: E 427 MET cc_start: 0.8565 (tmm) cc_final: 0.8282 (tmm) REVERT: E 554 GLU cc_start: 0.8137 (tt0) cc_final: 0.7755 (tm-30) REVERT: F 740 MET cc_start: 0.8554 (tmm) cc_final: 0.8248 (tmm) outliers start: 37 outliers final: 26 residues processed: 372 average time/residue: 0.5369 time to fit residues: 340.0468 Evaluate side-chains 370 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 339 time to evaluate : 5.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Y residue 208 ARG Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 0.6980 chunk 336 optimal weight: 1.9990 chunk 451 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 390 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 424 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 435 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 603 GLN E 602 ASN F 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090246 restraints weight = 111066.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091094 restraints weight = 70946.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092190 restraints weight = 55306.966| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 43852 Z= 0.159 Angle : 0.640 12.134 59392 Z= 0.299 Chirality : 0.043 0.221 6567 Planarity : 0.004 0.073 7737 Dihedral : 7.691 146.078 6027 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.24 % Favored : 92.45 % Rotamer: Outliers : 0.98 % Allowed : 17.63 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 5362 helix: 1.17 (0.11), residues: 2369 sheet: 0.34 (0.20), residues: 695 loop : -1.42 (0.14), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP Z 106 HIS 0.007 0.000 HIS F 404 PHE 0.043 0.001 PHE B 265 TYR 0.025 0.001 TYR F 244 ARG 0.004 0.000 ARG E 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7842.59 seconds wall clock time: 143 minutes 57.97 seconds (8637.97 seconds total)