Starting phenix.real_space_refine on Fri Mar 22 02:25:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/03_2024/7mdm_23775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/03_2024/7mdm_23775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/03_2024/7mdm_23775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/03_2024/7mdm_23775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/03_2024/7mdm_23775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/03_2024/7mdm_23775_updated.pdb" } resolution = 4.86 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= -0.001 sd= 0.075 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 12 5.49 5 S 172 5.16 5 C 20123 2.51 5 N 5597 2.21 5 O 6082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 392": "OD1" <-> "OD2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 599": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31986 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5513 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 662} Chain breaks: 2 Chain: "C" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5527 Classifications: {'peptide': 703} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 664} Chain breaks: 2 Chain: "D" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5527 Classifications: {'peptide': 703} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 664} Chain breaks: 2 Chain: "E" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5532 Classifications: {'peptide': 704} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 665} Chain breaks: 2 Chain: "A" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5513 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 662} Chain breaks: 2 Chain: "F" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4212 Classifications: {'peptide': 539} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 510} Chain breaks: 2 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.72, per 1000 atoms: 0.52 Number of scatterers: 31986 At special positions: 0 Unit cell: (104.52, 160.68, 171.6, 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 172 16.00 P 12 15.00 O 6082 8.00 N 5597 7.00 C 20123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.09 Conformation dependent library (CDL) restraints added in 5.3 seconds 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 34 sheets defined 36.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 131 through 139 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 333 removed outlier: 4.473A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 456 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 492 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 526 through 534 removed outlier: 3.969A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 567 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.602A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 removed outlier: 4.549A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 675 No H-bonds generated for 'chain 'B' and resid 672 through 675' Processing helix chain 'B' and resid 684 through 703 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.543A pdb=" N ARG B 753 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 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 91 Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 213 through 225 removed outlier: 4.466A 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 232 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 328 through 331 No H-bonds generated for 'chain 'C' and resid 328 through 331' Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.904A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 400 No H-bonds generated for 'chain 'C' and resid 397 through 400' Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 456 Processing helix chain 'C' and resid 483 through 498 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 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 580 through 583 No H-bonds generated for 'chain 'C' and resid 580 through 583' Processing helix chain 'C' and resid 600 through 607 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 684 through 702 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.972A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 92 removed outlier: 5.460A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 4.483A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 210 through 220 removed outlier: 4.156A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 282 through 296 removed outlier: 4.176A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.961A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'D' and resid 483 through 494 Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 544 through 551 removed outlier: 4.496A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 567 Processing helix chain 'D' and resid 579 through 583 Processing helix chain 'D' and resid 600 through 606 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 673 through 678 removed outlier: 4.517A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 703 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 86 through 92 removed outlier: 4.504A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) 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 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.372A pdb=" N PHE E 230 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 233 " --> pdb=" O PHE E 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 233' Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 274 No H-bonds generated for 'chain 'E' and resid 271 through 274' Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.658A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 319 through 325 removed outlier: 3.508A pdb=" N VAL E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 374 through 384 removed outlier: 5.259A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 449 through 456 Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 524 through 533 removed outlier: 3.664A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 553 removed outlier: 4.180A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 579 through 583 removed outlier: 3.887A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA E 583 " --> pdb=" O ASP E 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 579 through 583' Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.564A pdb=" N ARG E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 703 Processing helix chain 'E' and resid 733 through 739 Processing helix chain 'E' and resid 751 through 762 Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' 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 91 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 131 through 138 removed outlier: 5.067A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 213 through 225 removed outlier: 5.568A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 331 removed outlier: 5.036A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.849A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 485 through 494 removed outlier: 4.261A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.969A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 600 through 609 removed outlier: 4.419A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.763A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 684 through 703 removed outlier: 3.687A pdb=" N ILE A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 762 Processing helix chain 'F' and resid 213 through 224 removed outlier: 5.632A 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 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 291 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 331 removed outlier: 5.163A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.855A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 No H-bonds generated for 'chain 'F' and resid 399 through 402' Processing helix chain 'F' and resid 408 through 423 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 456 Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 removed outlier: 4.383A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.626A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.785A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.589A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 600 through 607 Processing helix chain 'F' and resid 650 through 663 removed outlier: 4.324A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 684 through 703 Processing helix chain 'F' and resid 734 through 740 Processing helix chain 'F' and resid 750 through 762 removed outlier: 3.559A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= B, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.638A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.636A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 469 through 471 removed outlier: 3.935A pdb=" N ILE B 540 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 575 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 577 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= G, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.081A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.771A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 153 through 156 Processing sheet with id= J, first strand: chain 'C' and resid 241 through 244 removed outlier: 7.021A pdb=" N ARG C 365 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N TYR C 244 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 367 " --> pdb=" O TYR C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 265 through 269 removed outlier: 3.520A pdb=" N PHE C 267 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 302 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 304 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 342 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE C 303 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N MET C 344 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 619 through 623 removed outlier: 4.131A pdb=" N VAL C 514 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN C 641 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR C 517 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 643 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 538 through 542 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 118 removed outlier: 4.134A pdb=" N HIS C 115 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.966A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.757A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 153 through 155 Processing sheet with id= R, first strand: chain 'D' and resid 241 through 244 removed outlier: 7.554A pdb=" N ARG D 365 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TYR D 244 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 367 " --> pdb=" O TYR D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.500A pdb=" N PHE D 267 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 302 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 539 through 543 removed outlier: 6.735A pdb=" N VAL D 573 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE D 542 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 575 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 514 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.679A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 38 through 41 removed outlier: 6.787A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 57 through 59 removed outlier: 3.573A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 151 through 155 removed outlier: 3.612A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 241 through 243 removed outlier: 3.570A pdb=" N ILE E 241 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 642 through 645 removed outlier: 8.507A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 645 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR E 517 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'A' and resid 27 through 30 Processing sheet with id= AB, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.657A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= AD, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.723A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.944A pdb=" N LEU A 242 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 367 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR A 244 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 469 through 471 removed outlier: 3.903A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 265 through 268 Processing sheet with id= AH, first strand: chain 'F' and resid 643 through 645 removed outlier: 3.745A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2433 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: 10.78 Time building geometry restraints manager: 14.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9073 1.33 - 1.46: 5643 1.46 - 1.58: 17504 1.58 - 1.70: 19 1.70 - 1.82: 277 Bond restraints: 32516 Sorted by residual: bond pdb=" C CYS A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.404 -0.071 8.40e-03 1.42e+04 7.11e+01 bond pdb=" CA GLU E 314 " pdb=" C GLU E 314 " ideal model delta sigma weight residual 1.523 1.589 -0.066 1.80e-02 3.09e+03 1.35e+01 bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.334 1.407 -0.074 2.34e-02 1.83e+03 9.87e+00 bond pdb=" C ASN A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.54e+00 bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.34e+00 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.23: 771 105.23 - 113.00: 16965 113.00 - 120.77: 15597 120.77 - 128.54: 10407 128.54 - 136.31: 202 Bond angle restraints: 43942 Sorted by residual: angle pdb=" C SER F 326 " pdb=" N GLN F 327 " pdb=" CA GLN F 327 " ideal model delta sigma weight residual 121.54 135.92 -14.38 1.91e+00 2.74e-01 5.67e+01 angle pdb=" N LYS F 211 " pdb=" CA LYS F 211 " pdb=" C LYS F 211 " ideal model delta sigma weight residual 114.56 105.37 9.19 1.27e+00 6.20e-01 5.24e+01 angle pdb=" C SER A 326 " pdb=" N GLN A 327 " pdb=" CA GLN A 327 " ideal model delta sigma weight residual 121.54 134.60 -13.06 1.91e+00 2.74e-01 4.67e+01 angle pdb=" CB MET F 740 " pdb=" CG MET F 740 " pdb=" SD MET F 740 " ideal model delta sigma weight residual 112.70 131.30 -18.60 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N ILE D 369 " pdb=" CA ILE D 369 " pdb=" C ILE D 369 " ideal model delta sigma weight residual 112.96 106.95 6.01 1.00e+00 1.00e+00 3.61e+01 ... (remaining 43937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 19630 32.98 - 65.97: 521 65.97 - 98.95: 35 98.95 - 131.94: 6 131.94 - 164.92: 1 Dihedral angle restraints: 20193 sinusoidal: 8483 harmonic: 11710 Sorted by residual: dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N LEU B 96 " pdb=" CA LEU B 96 " ideal model delta harmonic sigma weight residual 180.00 129.94 50.06 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 104.92 -164.92 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" CA LEU A 331 " pdb=" C LEU A 331 " pdb=" N MET A 332 " pdb=" CA MET A 332 " ideal model delta harmonic sigma weight residual 180.00 147.39 32.61 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 20190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4160 0.089 - 0.179: 712 0.179 - 0.268: 79 0.268 - 0.358: 21 0.358 - 0.447: 6 Chirality restraints: 4978 Sorted by residual: chirality pdb=" CB VAL A 108 " pdb=" CA VAL A 108 " pdb=" CG1 VAL A 108 " pdb=" CG2 VAL A 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB ILE E 303 " pdb=" CA ILE E 303 " pdb=" CG1 ILE E 303 " pdb=" CG2 ILE E 303 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE E 241 " pdb=" CA ILE E 241 " pdb=" CG1 ILE E 241 " pdb=" CG2 ILE E 241 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 4975 not shown) Planarity restraints: 5767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 495 " 0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 496 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 496 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 496 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLN B 327 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN B 327 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 328 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 95 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ARG B 95 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG B 95 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 96 " 0.019 2.00e-02 2.50e+03 ... (remaining 5764 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7606 2.79 - 3.32: 30925 3.32 - 3.84: 58124 3.84 - 4.37: 65280 4.37 - 4.90: 103118 Nonbonded interactions: 265053 Sorted by model distance: nonbonded pdb=" O VAL D 258 " pdb=" OG1 THR D 262 " model vdw 2.261 2.440 nonbonded pdb=" O ILE D 274 " pdb=" OG SER D 282 " model vdw 2.274 2.440 nonbonded pdb=" O MET A 757 " pdb=" OG1 THR A 761 " model vdw 2.280 2.440 nonbonded pdb=" O LEU D 381 " pdb=" OG1 THR D 385 " model vdw 2.293 2.440 nonbonded pdb=" O PRO D 246 " pdb=" OG1 THR D 249 " model vdw 2.296 2.440 ... (remaining 265048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 25 through 582 or resid 598 through 763 or resid 901)) selection = (chain 'D' and (resid 25 through 582 or resid 598 through 763 or resid 901)) selection = (chain 'E' and (resid 25 through 582 or resid 598 through 763 or resid 901)) } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.840 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 83.620 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.190 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32516 Z= 0.327 Angle : 1.189 18.595 43942 Z= 0.623 Chirality : 0.070 0.447 4978 Planarity : 0.008 0.086 5767 Dihedral : 15.375 164.919 12577 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.11), residues: 4015 helix: -2.92 (0.09), residues: 1644 sheet: -1.61 (0.23), residues: 442 loop : -1.87 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 551 HIS 0.011 0.002 HIS B 226 PHE 0.033 0.002 PHE E 302 TYR 0.031 0.002 TYR A 495 ARG 0.019 0.001 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1035 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9259 (mmm) cc_final: 0.8871 (mmm) REVERT: B 135 LEU cc_start: 0.9184 (tt) cc_final: 0.8698 (mm) REVERT: B 256 ARG cc_start: 0.8771 (tpt90) cc_final: 0.8541 (mmm160) REVERT: B 302 PHE cc_start: 0.8322 (t80) cc_final: 0.7936 (t80) REVERT: B 305 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 363 PHE cc_start: 0.8296 (m-10) cc_final: 0.8085 (m-80) REVERT: B 366 GLU cc_start: 0.8566 (pm20) cc_final: 0.8052 (pm20) REVERT: B 369 ILE cc_start: 0.9093 (tt) cc_final: 0.8834 (tp) REVERT: B 381 LEU cc_start: 0.9479 (mt) cc_final: 0.9119 (mt) REVERT: B 388 MET cc_start: 0.8195 (mmp) cc_final: 0.7385 (mmm) REVERT: B 514 VAL cc_start: 0.9004 (p) cc_final: 0.8732 (p) REVERT: B 516 PHE cc_start: 0.9308 (m-80) cc_final: 0.8717 (m-80) REVERT: B 517 TYR cc_start: 0.8232 (p90) cc_final: 0.7330 (p90) REVERT: B 524 LYS cc_start: 0.8819 (mttt) cc_final: 0.7919 (ttpt) REVERT: B 538 ASN cc_start: 0.9099 (t0) cc_final: 0.8130 (m110) REVERT: B 542 ILE cc_start: 0.8968 (mp) cc_final: 0.8643 (mp) REVERT: B 609 ASP cc_start: 0.9033 (m-30) cc_final: 0.8684 (m-30) REVERT: B 611 MET cc_start: 0.8966 (pmm) cc_final: 0.8682 (pmm) REVERT: B 674 PHE cc_start: 0.8311 (m-80) cc_final: 0.8052 (m-80) REVERT: B 678 MET cc_start: 0.7881 (mtt) cc_final: 0.7359 (ptt) REVERT: B 736 PHE cc_start: 0.8628 (m-10) cc_final: 0.8322 (m-10) REVERT: B 756 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8117 (pp20) REVERT: C 148 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8522 (tptp) REVERT: C 162 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 163 PHE cc_start: 0.8891 (m-80) cc_final: 0.8139 (m-80) REVERT: C 200 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9015 (tp30) REVERT: C 203 TYR cc_start: 0.8514 (m-10) cc_final: 0.7212 (m-80) REVERT: C 216 ILE cc_start: 0.9470 (pt) cc_final: 0.9222 (mm) REVERT: C 243 LEU cc_start: 0.9743 (mt) cc_final: 0.8968 (mt) REVERT: C 251 LYS cc_start: 0.9571 (ptpt) cc_final: 0.9338 (mtmm) REVERT: C 260 ASN cc_start: 0.8860 (m110) cc_final: 0.8117 (m110) REVERT: C 269 ILE cc_start: 0.9182 (mp) cc_final: 0.8916 (mp) REVERT: C 285 ASN cc_start: 0.8878 (t160) cc_final: 0.8388 (t0) REVERT: C 288 LYS cc_start: 0.9259 (tmtt) cc_final: 0.8916 (pptt) REVERT: C 291 GLU cc_start: 0.9162 (mp0) cc_final: 0.8634 (pm20) REVERT: C 352 SER cc_start: 0.9306 (m) cc_final: 0.9045 (t) REVERT: C 420 LEU cc_start: 0.9699 (mt) cc_final: 0.9444 (mt) REVERT: C 423 ILE cc_start: 0.9541 (tp) cc_final: 0.9143 (tt) REVERT: C 432 LEU cc_start: 0.8427 (mt) cc_final: 0.7751 (mm) REVERT: C 438 ASP cc_start: 0.8482 (t70) cc_final: 0.8159 (t0) REVERT: C 441 VAL cc_start: 0.8925 (p) cc_final: 0.8663 (p) REVERT: C 442 MET cc_start: 0.8962 (mmp) cc_final: 0.8652 (tpp) REVERT: C 449 MET cc_start: 0.8808 (mmp) cc_final: 0.8101 (mmp) REVERT: C 515 LEU cc_start: 0.8940 (mm) cc_final: 0.8682 (mm) REVERT: C 564 ASP cc_start: 0.8926 (m-30) cc_final: 0.8618 (t0) REVERT: C 609 ASP cc_start: 0.9019 (m-30) cc_final: 0.8614 (m-30) REVERT: C 696 LYS cc_start: 0.9547 (tppt) cc_final: 0.9314 (tttt) REVERT: D 28 VAL cc_start: 0.7316 (t) cc_final: 0.7099 (t) REVERT: D 135 LEU cc_start: 0.8230 (mt) cc_final: 0.7496 (tt) REVERT: D 139 PHE cc_start: 0.8615 (m-80) cc_final: 0.8391 (m-80) REVERT: D 199 ASN cc_start: 0.8532 (p0) cc_final: 0.8023 (p0) REVERT: D 219 MET cc_start: 0.7997 (pmm) cc_final: 0.7425 (pmm) REVERT: D 242 LEU cc_start: 0.9225 (mm) cc_final: 0.8407 (mm) REVERT: D 265 PHE cc_start: 0.7630 (t80) cc_final: 0.6969 (t80) REVERT: D 267 PHE cc_start: 0.8320 (t80) cc_final: 0.8081 (t80) REVERT: D 269 ILE cc_start: 0.9211 (mt) cc_final: 0.8727 (mt) REVERT: D 275 MET cc_start: 0.9438 (ptp) cc_final: 0.9088 (ptp) REVERT: D 302 PHE cc_start: 0.8253 (t80) cc_final: 0.7836 (t80) REVERT: D 315 LYS cc_start: 0.6958 (tptt) cc_final: 0.6242 (tppt) REVERT: D 319 GLU cc_start: 0.9097 (pp20) cc_final: 0.8832 (tm-30) REVERT: D 344 MET cc_start: 0.8732 (ttp) cc_final: 0.8524 (ttp) REVERT: D 388 MET cc_start: 0.8572 (mpp) cc_final: 0.8154 (mpp) REVERT: D 397 GLU cc_start: 0.8992 (mp0) cc_final: 0.8555 (mm-30) REVERT: D 414 LEU cc_start: 0.9112 (tt) cc_final: 0.8806 (tt) REVERT: D 476 TRP cc_start: 0.6295 (m100) cc_final: 0.6030 (m100) REVERT: D 561 GLU cc_start: 0.8169 (pt0) cc_final: 0.7675 (pt0) REVERT: D 562 ILE cc_start: 0.9325 (tp) cc_final: 0.8978 (pt) REVERT: D 575 PHE cc_start: 0.8474 (t80) cc_final: 0.7965 (t80) REVERT: D 656 ILE cc_start: 0.9530 (mt) cc_final: 0.9286 (tp) REVERT: D 700 ARG cc_start: 0.9072 (pmt-80) cc_final: 0.8740 (ptm160) REVERT: E 66 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6377 (mm-30) REVERT: E 86 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7934 (ttp-170) REVERT: E 216 ILE cc_start: 0.9307 (pt) cc_final: 0.8896 (tp) REVERT: E 218 GLU cc_start: 0.9030 (tt0) cc_final: 0.8573 (tm-30) REVERT: E 219 MET cc_start: 0.8894 (ppp) cc_final: 0.8675 (ppp) REVERT: E 269 ILE cc_start: 0.9020 (mp) cc_final: 0.8526 (mp) REVERT: E 291 GLU cc_start: 0.9180 (mp0) cc_final: 0.8859 (mp0) REVERT: E 379 GLU cc_start: 0.9046 (pm20) cc_final: 0.8584 (tp30) REVERT: E 383 ILE cc_start: 0.9571 (mt) cc_final: 0.9286 (mt) REVERT: E 388 MET cc_start: 0.8756 (mmp) cc_final: 0.8546 (mmm) REVERT: E 417 GLU cc_start: 0.9410 (pm20) cc_final: 0.9098 (pm20) REVERT: E 449 MET cc_start: 0.8988 (mmp) cc_final: 0.8524 (mmp) REVERT: E 450 ASP cc_start: 0.8602 (p0) cc_final: 0.8379 (p0) REVERT: E 452 PHE cc_start: 0.8239 (m-10) cc_final: 0.8010 (m-80) REVERT: E 517 TYR cc_start: 0.6672 (p90) cc_final: 0.6399 (p90) REVERT: E 538 ASN cc_start: 0.9126 (t0) cc_final: 0.8607 (m110) REVERT: E 550 MET cc_start: 0.4341 (mmm) cc_final: 0.2849 (tpp) REVERT: E 560 ARG cc_start: 0.9529 (ttt-90) cc_final: 0.9076 (tpp-160) REVERT: E 563 PHE cc_start: 0.9232 (m-10) cc_final: 0.8849 (m-80) REVERT: E 572 CYS cc_start: 0.8157 (p) cc_final: 0.7201 (p) REVERT: E 697 LEU cc_start: 0.8532 (mt) cc_final: 0.8299 (tp) REVERT: E 734 ASP cc_start: 0.9593 (m-30) cc_final: 0.9353 (p0) REVERT: E 736 PHE cc_start: 0.8797 (m-10) cc_final: 0.8310 (m-10) REVERT: E 741 ARG cc_start: 0.8865 (tpm170) cc_final: 0.8476 (mmm-85) REVERT: A 26 LEU cc_start: 0.7949 (mm) cc_final: 0.7614 (mm) REVERT: A 135 LEU cc_start: 0.9192 (tp) cc_final: 0.8903 (tp) REVERT: A 155 ARG cc_start: 0.8346 (mpp-170) cc_final: 0.7697 (ttm-80) REVERT: A 158 MET cc_start: 0.7657 (tmm) cc_final: 0.7189 (tmm) REVERT: A 163 PHE cc_start: 0.8551 (m-10) cc_final: 0.7631 (m-80) REVERT: A 216 ILE cc_start: 0.9431 (pt) cc_final: 0.9053 (mm) REVERT: A 221 GLU cc_start: 0.8434 (pm20) cc_final: 0.8054 (pp20) REVERT: A 237 PRO cc_start: 0.8255 (Cg_endo) cc_final: 0.7443 (Cg_exo) REVERT: A 243 LEU cc_start: 0.9320 (mm) cc_final: 0.9086 (mm) REVERT: A 244 TYR cc_start: 0.7841 (p90) cc_final: 0.7182 (p90) REVERT: A 253 LEU cc_start: 0.8904 (mt) cc_final: 0.8284 (mt) REVERT: A 344 MET cc_start: 0.7859 (mmp) cc_final: 0.7126 (mmp) REVERT: A 349 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8312 (ttm-80) REVERT: A 366 GLU cc_start: 0.7136 (tt0) cc_final: 0.6606 (tt0) REVERT: A 375 THR cc_start: 0.9284 (p) cc_final: 0.9039 (t) REVERT: A 381 LEU cc_start: 0.8967 (tt) cc_final: 0.8472 (tt) REVERT: A 386 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8640 (mmmt) REVERT: A 395 ASP cc_start: 0.8194 (m-30) cc_final: 0.7892 (m-30) REVERT: A 396 LEU cc_start: 0.8490 (mt) cc_final: 0.8253 (mm) REVERT: A 516 PHE cc_start: 0.9018 (m-80) cc_final: 0.8162 (m-80) REVERT: A 541 SER cc_start: 0.9096 (t) cc_final: 0.8634 (t) REVERT: A 549 THR cc_start: 0.8989 (t) cc_final: 0.8769 (t) REVERT: A 564 ASP cc_start: 0.9158 (t0) cc_final: 0.8721 (t0) REVERT: A 644 TYR cc_start: 0.6641 (t80) cc_final: 0.6207 (t80) REVERT: A 651 LYS cc_start: 0.9309 (pttt) cc_final: 0.8949 (tmtt) REVERT: A 752 ILE cc_start: 0.8714 (tt) cc_final: 0.8103 (pt) REVERT: F 204 ASP cc_start: 0.8939 (m-30) cc_final: 0.8262 (p0) REVERT: F 222 LEU cc_start: 0.9266 (tp) cc_final: 0.8403 (tp) REVERT: F 337 GLN cc_start: 0.6674 (mm110) cc_final: 0.4681 (tp40) REVERT: F 351 ASN cc_start: 0.9394 (p0) cc_final: 0.8955 (p0) REVERT: F 357 LEU cc_start: 0.9317 (tp) cc_final: 0.8786 (tp) REVERT: F 364 ASP cc_start: 0.7094 (m-30) cc_final: 0.6750 (m-30) REVERT: F 366 GLU cc_start: 0.7803 (mp0) cc_final: 0.7546 (pm20) REVERT: F 378 LEU cc_start: 0.9749 (tp) cc_final: 0.9500 (tp) REVERT: F 423 ILE cc_start: 0.8429 (pt) cc_final: 0.8166 (mm) REVERT: F 427 MET cc_start: 0.7306 (tpt) cc_final: 0.5653 (tpp) REVERT: F 465 ARG cc_start: 0.6534 (tpt170) cc_final: 0.6076 (ptm160) REVERT: F 470 GLU cc_start: 0.8047 (pp20) cc_final: 0.7411 (pm20) REVERT: F 508 MET cc_start: 0.1107 (ttm) cc_final: 0.0729 (ttm) REVERT: F 609 ASP cc_start: 0.9356 (m-30) cc_final: 0.8755 (m-30) REVERT: F 611 MET cc_start: 0.8384 (pmm) cc_final: 0.8016 (pmm) REVERT: F 678 MET cc_start: 0.7675 (tpt) cc_final: 0.7419 (ttm) REVERT: F 737 GLU cc_start: 0.7097 (tp30) cc_final: 0.6620 (mt-10) REVERT: F 740 MET cc_start: 0.4073 (pmm) cc_final: 0.2914 (pmm) outliers start: 1 outliers final: 0 residues processed: 1036 average time/residue: 0.4908 time to fit residues: 767.0018 Evaluate side-chains 671 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 365 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN B 760 GLN C 183 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS C 458 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN D 443 ASN D 458 GLN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 401 ASN E 692 GLN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN F 260 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32516 Z= 0.290 Angle : 0.786 8.807 43942 Z= 0.403 Chirality : 0.047 0.192 4978 Planarity : 0.006 0.079 5767 Dihedral : 8.198 157.496 4446 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.12), residues: 4015 helix: -1.77 (0.11), residues: 1678 sheet: -1.57 (0.22), residues: 478 loop : -1.54 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 476 HIS 0.011 0.002 HIS A 735 PHE 0.034 0.002 PHE A 563 TYR 0.020 0.002 TYR C 755 ARG 0.019 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 782 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9331 (pttm) cc_final: 0.8844 (pttm) REVERT: B 84 MET cc_start: 0.9274 (mmm) cc_final: 0.8950 (mmm) REVERT: B 152 PHE cc_start: 0.7287 (p90) cc_final: 0.6895 (p90) REVERT: B 200 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 302 PHE cc_start: 0.8469 (t80) cc_final: 0.7785 (t80) REVERT: B 305 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 332 MET cc_start: 0.8710 (tpt) cc_final: 0.8503 (tmm) REVERT: B 344 MET cc_start: 0.8932 (tpt) cc_final: 0.8700 (tmm) REVERT: B 363 PHE cc_start: 0.8668 (m-10) cc_final: 0.7757 (m-80) REVERT: B 366 GLU cc_start: 0.8959 (pm20) cc_final: 0.8367 (pm20) REVERT: B 379 GLU cc_start: 0.9199 (tp30) cc_final: 0.8694 (pt0) REVERT: B 388 MET cc_start: 0.8409 (mmp) cc_final: 0.7880 (mmm) REVERT: B 514 VAL cc_start: 0.8179 (p) cc_final: 0.7713 (p) REVERT: B 538 ASN cc_start: 0.9226 (t0) cc_final: 0.8803 (t0) REVERT: B 609 ASP cc_start: 0.9121 (m-30) cc_final: 0.8894 (m-30) REVERT: B 678 MET cc_start: 0.8021 (mtt) cc_final: 0.6977 (ptt) REVERT: B 736 PHE cc_start: 0.8665 (m-10) cc_final: 0.8435 (m-10) REVERT: B 757 MET cc_start: 0.8357 (ttt) cc_final: 0.8065 (tmm) REVERT: C 84 MET cc_start: 0.8939 (mpp) cc_final: 0.8578 (mpp) REVERT: C 131 PHE cc_start: 0.7975 (m-10) cc_final: 0.7717 (m-10) REVERT: C 148 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8783 (tptp) REVERT: C 154 VAL cc_start: 0.8429 (t) cc_final: 0.8213 (t) REVERT: C 162 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 163 PHE cc_start: 0.8686 (m-80) cc_final: 0.8093 (m-80) REVERT: C 190 LYS cc_start: 0.9635 (pptt) cc_final: 0.9266 (pptt) REVERT: C 200 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9000 (tp30) REVERT: C 221 GLU cc_start: 0.8392 (pt0) cc_final: 0.7860 (pp20) REVERT: C 251 LYS cc_start: 0.9552 (ptpt) cc_final: 0.9306 (mtmm) REVERT: C 269 ILE cc_start: 0.9258 (mp) cc_final: 0.9046 (mp) REVERT: C 288 LYS cc_start: 0.9272 (tmtt) cc_final: 0.8962 (pptt) REVERT: C 306 LEU cc_start: 0.9329 (mm) cc_final: 0.9083 (mm) REVERT: C 333 ASP cc_start: 0.8224 (t0) cc_final: 0.7986 (m-30) REVERT: C 352 SER cc_start: 0.9365 (m) cc_final: 0.9105 (t) REVERT: C 362 ARG cc_start: 0.7813 (mpp-170) cc_final: 0.7342 (mpt180) REVERT: C 378 LEU cc_start: 0.9252 (mt) cc_final: 0.8838 (pp) REVERT: C 406 HIS cc_start: 0.8200 (m-70) cc_final: 0.7860 (m170) REVERT: C 449 MET cc_start: 0.8807 (mmp) cc_final: 0.7971 (mmp) REVERT: C 515 LEU cc_start: 0.8317 (mm) cc_final: 0.7933 (mm) REVERT: C 609 ASP cc_start: 0.9128 (m-30) cc_final: 0.8526 (m-30) REVERT: C 639 LEU cc_start: 0.6533 (mm) cc_final: 0.6226 (mm) REVERT: C 696 LYS cc_start: 0.9702 (tppt) cc_final: 0.9405 (mptt) REVERT: D 135 LEU cc_start: 0.8449 (mt) cc_final: 0.7953 (mt) REVERT: D 139 PHE cc_start: 0.8822 (m-80) cc_final: 0.8467 (m-80) REVERT: D 158 MET cc_start: 0.7430 (ppp) cc_final: 0.7107 (ppp) REVERT: D 199 ASN cc_start: 0.8919 (p0) cc_final: 0.8535 (p0) REVERT: D 219 MET cc_start: 0.8355 (pmm) cc_final: 0.7596 (pmm) REVERT: D 241 ILE cc_start: 0.8395 (tp) cc_final: 0.8073 (tp) REVERT: D 243 LEU cc_start: 0.9394 (mm) cc_final: 0.9114 (mm) REVERT: D 265 PHE cc_start: 0.8108 (t80) cc_final: 0.7588 (t80) REVERT: D 295 LYS cc_start: 0.9329 (ptpt) cc_final: 0.9100 (mtmt) REVERT: D 301 ILE cc_start: 0.8971 (mp) cc_final: 0.8601 (mp) REVERT: D 302 PHE cc_start: 0.8371 (t80) cc_final: 0.7894 (t80) REVERT: D 303 ILE cc_start: 0.9572 (mp) cc_final: 0.9363 (tp) REVERT: D 315 LYS cc_start: 0.6890 (tptt) cc_final: 0.6570 (tppt) REVERT: D 319 GLU cc_start: 0.9529 (pp20) cc_final: 0.9301 (pp20) REVERT: D 366 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7939 (mp0) REVERT: D 383 ILE cc_start: 0.9131 (pt) cc_final: 0.8789 (pt) REVERT: D 388 MET cc_start: 0.8829 (mpp) cc_final: 0.8558 (mpp) REVERT: D 404 HIS cc_start: 0.8470 (p-80) cc_final: 0.7911 (p-80) REVERT: D 449 MET cc_start: 0.8976 (mmp) cc_final: 0.8755 (mmp) REVERT: D 476 TRP cc_start: 0.6857 (m100) cc_final: 0.6095 (m100) REVERT: D 495 TYR cc_start: 0.6065 (t80) cc_final: 0.5559 (t80) REVERT: D 508 MET cc_start: 0.2222 (ptt) cc_final: 0.1101 (ptt) REVERT: D 515 LEU cc_start: 0.9187 (mm) cc_final: 0.8881 (mm) REVERT: D 516 PHE cc_start: 0.8755 (m-80) cc_final: 0.8408 (m-80) REVERT: D 549 THR cc_start: 0.6939 (p) cc_final: 0.6521 (p) REVERT: D 550 MET cc_start: 0.6218 (pmm) cc_final: 0.5660 (pmm) REVERT: D 562 ILE cc_start: 0.9214 (tp) cc_final: 0.8985 (pt) REVERT: D 575 PHE cc_start: 0.8715 (t80) cc_final: 0.7926 (t80) REVERT: D 678 MET cc_start: 0.3789 (ptt) cc_final: 0.3556 (ptt) REVERT: D 700 ARG cc_start: 0.9176 (pmt-80) cc_final: 0.8596 (ptm160) REVERT: E 28 VAL cc_start: 0.8492 (m) cc_final: 0.8150 (m) REVERT: E 66 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6371 (mm-30) REVERT: E 218 GLU cc_start: 0.9091 (tt0) cc_final: 0.8808 (tm-30) REVERT: E 219 MET cc_start: 0.9151 (ppp) cc_final: 0.8433 (ptm) REVERT: E 244 TYR cc_start: 0.8410 (p90) cc_final: 0.8127 (p90) REVERT: E 275 MET cc_start: 0.9269 (mpp) cc_final: 0.9052 (mpp) REVERT: E 291 GLU cc_start: 0.9257 (mp0) cc_final: 0.8513 (tp30) REVERT: E 305 GLU cc_start: 0.7942 (mp0) cc_final: 0.7515 (mp0) REVERT: E 378 LEU cc_start: 0.9420 (pp) cc_final: 0.9125 (pp) REVERT: E 388 MET cc_start: 0.8464 (mmp) cc_final: 0.8228 (mmm) REVERT: E 449 MET cc_start: 0.9138 (mmp) cc_final: 0.8515 (mmp) REVERT: E 451 ASP cc_start: 0.8417 (m-30) cc_final: 0.8181 (m-30) REVERT: E 452 PHE cc_start: 0.7934 (m-80) cc_final: 0.7539 (m-80) REVERT: E 470 GLU cc_start: 0.8705 (tt0) cc_final: 0.7826 (tm-30) REVERT: E 538 ASN cc_start: 0.9044 (t0) cc_final: 0.8450 (m110) REVERT: E 542 ILE cc_start: 0.9148 (tp) cc_final: 0.8916 (tp) REVERT: E 550 MET cc_start: 0.3679 (mmm) cc_final: 0.2431 (tpp) REVERT: E 560 ARG cc_start: 0.9509 (ttt-90) cc_final: 0.9184 (tpp80) REVERT: E 563 PHE cc_start: 0.9220 (m-10) cc_final: 0.8821 (m-80) REVERT: E 564 ASP cc_start: 0.9155 (m-30) cc_final: 0.8782 (m-30) REVERT: E 572 CYS cc_start: 0.7078 (p) cc_final: 0.6707 (p) REVERT: E 609 ASP cc_start: 0.8099 (t0) cc_final: 0.7897 (t0) REVERT: E 736 PHE cc_start: 0.8821 (m-10) cc_final: 0.8504 (m-10) REVERT: A 64 ARG cc_start: 0.8706 (tpt90) cc_final: 0.8242 (tpp-160) REVERT: A 135 LEU cc_start: 0.9153 (tp) cc_final: 0.8870 (tp) REVERT: A 158 MET cc_start: 0.8112 (tmm) cc_final: 0.7900 (tmm) REVERT: A 163 PHE cc_start: 0.8703 (m-10) cc_final: 0.7933 (m-80) REVERT: A 229 LEU cc_start: 0.8863 (mt) cc_final: 0.8601 (mp) REVERT: A 237 PRO cc_start: 0.8046 (Cg_endo) cc_final: 0.7299 (Cg_exo) REVERT: A 241 ILE cc_start: 0.8805 (tp) cc_final: 0.8220 (tp) REVERT: A 243 LEU cc_start: 0.9232 (mm) cc_final: 0.8896 (mm) REVERT: A 253 LEU cc_start: 0.9513 (mt) cc_final: 0.8855 (mt) REVERT: A 304 ASP cc_start: 0.8211 (p0) cc_final: 0.7716 (p0) REVERT: A 344 MET cc_start: 0.8570 (mmp) cc_final: 0.7613 (mmp) REVERT: A 375 THR cc_start: 0.9224 (p) cc_final: 0.8520 (t) REVERT: A 388 MET cc_start: 0.7759 (mpp) cc_final: 0.7536 (mpp) REVERT: A 423 ILE cc_start: 0.8758 (pt) cc_final: 0.8549 (pt) REVERT: A 459 SER cc_start: 0.9474 (t) cc_final: 0.9177 (m) REVERT: A 516 PHE cc_start: 0.9046 (m-80) cc_final: 0.8132 (m-80) REVERT: A 651 LYS cc_start: 0.9547 (pttt) cc_final: 0.9116 (tmtt) REVERT: A 752 ILE cc_start: 0.8232 (tt) cc_final: 0.8013 (pt) REVERT: F 204 ASP cc_start: 0.8815 (m-30) cc_final: 0.8130 (p0) REVERT: F 222 LEU cc_start: 0.9455 (tp) cc_final: 0.8541 (tp) REVERT: F 242 LEU cc_start: 0.9302 (mt) cc_final: 0.8969 (mt) REVERT: F 253 LEU cc_start: 0.9736 (mm) cc_final: 0.9485 (mm) REVERT: F 269 ILE cc_start: 0.9593 (mt) cc_final: 0.8797 (mt) REVERT: F 337 GLN cc_start: 0.7243 (mm110) cc_final: 0.5094 (tp40) REVERT: F 348 ASN cc_start: 0.9111 (t0) cc_final: 0.8754 (p0) REVERT: F 351 ASN cc_start: 0.9372 (p0) cc_final: 0.9131 (p0) REVERT: F 353 ILE cc_start: 0.9097 (mm) cc_final: 0.8846 (mp) REVERT: F 368 ASP cc_start: 0.8946 (t0) cc_final: 0.8691 (t0) REVERT: F 442 MET cc_start: 0.8413 (mmp) cc_final: 0.7426 (ptt) REVERT: F 470 GLU cc_start: 0.8106 (pp20) cc_final: 0.7561 (pm20) REVERT: F 495 TYR cc_start: 0.8790 (m-80) cc_final: 0.8183 (m-80) REVERT: F 517 TYR cc_start: 0.9347 (p90) cc_final: 0.9034 (p90) REVERT: F 565 LYS cc_start: 0.9254 (ptmm) cc_final: 0.8931 (pptt) REVERT: F 608 MET cc_start: 0.7761 (ptp) cc_final: 0.7558 (ptm) REVERT: F 609 ASP cc_start: 0.9218 (m-30) cc_final: 0.8827 (m-30) REVERT: F 611 MET cc_start: 0.8037 (pmm) cc_final: 0.7402 (pmm) REVERT: F 678 MET cc_start: 0.8424 (tpt) cc_final: 0.8124 (mtp) REVERT: F 740 MET cc_start: 0.5125 (pmm) cc_final: 0.4136 (pmm) outliers start: 6 outliers final: 2 residues processed: 786 average time/residue: 0.4876 time to fit residues: 585.5866 Evaluate side-chains 581 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 579 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 366 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 326 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 568 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32516 Z= 0.232 Angle : 0.734 17.182 43942 Z= 0.368 Chirality : 0.048 0.202 4978 Planarity : 0.005 0.075 5767 Dihedral : 7.993 169.095 4446 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.13), residues: 4015 helix: -1.40 (0.12), residues: 1665 sheet: -1.47 (0.23), residues: 475 loop : -1.43 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 551 HIS 0.010 0.001 HIS A 735 PHE 0.027 0.002 PHE B 563 TYR 0.018 0.002 TYR C 755 ARG 0.017 0.001 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 759 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8182 (mmp) cc_final: 0.7792 (mmm) REVERT: B 63 LYS cc_start: 0.9402 (pttm) cc_final: 0.8783 (pttm) REVERT: B 81 LYS cc_start: 0.8746 (tptt) cc_final: 0.8250 (tppt) REVERT: B 84 MET cc_start: 0.9150 (mmm) cc_final: 0.8814 (mmm) REVERT: B 200 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8258 (mt-10) REVERT: B 220 VAL cc_start: 0.9598 (m) cc_final: 0.9338 (m) REVERT: B 302 PHE cc_start: 0.8371 (t80) cc_final: 0.6870 (t80) REVERT: B 305 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 344 MET cc_start: 0.9061 (tpt) cc_final: 0.8798 (tpt) REVERT: B 363 PHE cc_start: 0.8699 (m-10) cc_final: 0.7893 (m-10) REVERT: B 366 GLU cc_start: 0.8811 (pm20) cc_final: 0.8298 (pm20) REVERT: B 388 MET cc_start: 0.8360 (mmp) cc_final: 0.7838 (mmm) REVERT: B 426 LYS cc_start: 0.9579 (mptt) cc_final: 0.9342 (mmtt) REVERT: B 514 VAL cc_start: 0.8230 (p) cc_final: 0.7639 (p) REVERT: B 517 TYR cc_start: 0.8116 (p90) cc_final: 0.7854 (p90) REVERT: B 538 ASN cc_start: 0.9224 (t0) cc_final: 0.8864 (t0) REVERT: B 620 ILE cc_start: 0.9276 (mp) cc_final: 0.8889 (mp) REVERT: B 649 ASP cc_start: 0.8241 (p0) cc_final: 0.8004 (p0) REVERT: B 671 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8372 (p0) REVERT: B 674 PHE cc_start: 0.9237 (m-80) cc_final: 0.8911 (m-10) REVERT: B 678 MET cc_start: 0.7614 (mtt) cc_final: 0.6922 (ptt) REVERT: B 736 PHE cc_start: 0.8619 (m-10) cc_final: 0.8305 (m-10) REVERT: B 757 MET cc_start: 0.8332 (ttt) cc_final: 0.8119 (tmm) REVERT: C 59 LEU cc_start: 0.8429 (tt) cc_final: 0.8205 (tt) REVERT: C 84 MET cc_start: 0.8992 (mpp) cc_final: 0.8531 (mpp) REVERT: C 117 LEU cc_start: 0.8383 (mt) cc_final: 0.7831 (tp) REVERT: C 131 PHE cc_start: 0.7899 (m-10) cc_final: 0.7503 (m-10) REVERT: C 154 VAL cc_start: 0.8382 (t) cc_final: 0.8181 (t) REVERT: C 162 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8019 (tm-30) REVERT: C 163 PHE cc_start: 0.8669 (m-80) cc_final: 0.8072 (m-80) REVERT: C 190 LYS cc_start: 0.9647 (pptt) cc_final: 0.9376 (pptt) REVERT: C 200 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9097 (tp30) REVERT: C 203 TYR cc_start: 0.8199 (m-10) cc_final: 0.7590 (m-80) REVERT: C 221 GLU cc_start: 0.8275 (pt0) cc_final: 0.7864 (pp20) REVERT: C 260 ASN cc_start: 0.8667 (m110) cc_final: 0.8181 (m110) REVERT: C 285 ASN cc_start: 0.8647 (t0) cc_final: 0.8013 (t0) REVERT: C 288 LYS cc_start: 0.9269 (tttt) cc_final: 0.8901 (pttp) REVERT: C 291 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9139 (pt0) REVERT: C 333 ASP cc_start: 0.8279 (t0) cc_final: 0.8035 (m-30) REVERT: C 352 SER cc_start: 0.9330 (m) cc_final: 0.9083 (t) REVERT: C 442 MET cc_start: 0.9171 (mmp) cc_final: 0.8878 (tpp) REVERT: C 449 MET cc_start: 0.8670 (mmp) cc_final: 0.7964 (mmp) REVERT: C 515 LEU cc_start: 0.8850 (mm) cc_final: 0.8556 (mm) REVERT: C 609 ASP cc_start: 0.9100 (m-30) cc_final: 0.8529 (m-30) REVERT: C 639 LEU cc_start: 0.6510 (mm) cc_final: 0.6204 (mm) REVERT: C 662 ARG cc_start: 0.9090 (tmm160) cc_final: 0.8880 (ttp80) REVERT: C 696 LYS cc_start: 0.9727 (tppt) cc_final: 0.9261 (mttt) REVERT: D 33 ASN cc_start: 0.7149 (t0) cc_final: 0.6149 (t0) REVERT: D 35 ASP cc_start: 0.8493 (t0) cc_final: 0.7664 (m-30) REVERT: D 135 LEU cc_start: 0.8384 (mt) cc_final: 0.7906 (mt) REVERT: D 139 PHE cc_start: 0.8803 (m-80) cc_final: 0.8460 (m-80) REVERT: D 158 MET cc_start: 0.6957 (ppp) cc_final: 0.6624 (ppp) REVERT: D 199 ASN cc_start: 0.8982 (p0) cc_final: 0.8516 (p0) REVERT: D 219 MET cc_start: 0.8363 (pmm) cc_final: 0.7562 (pmm) REVERT: D 221 GLU cc_start: 0.8590 (pm20) cc_final: 0.8390 (pm20) REVERT: D 265 PHE cc_start: 0.7982 (t80) cc_final: 0.7563 (t80) REVERT: D 268 LEU cc_start: 0.9488 (tt) cc_final: 0.8957 (tt) REVERT: D 288 LYS cc_start: 0.9339 (pptt) cc_final: 0.9065 (pptt) REVERT: D 291 GLU cc_start: 0.8600 (pp20) cc_final: 0.8357 (pp20) REVERT: D 301 ILE cc_start: 0.9228 (mp) cc_final: 0.8948 (mp) REVERT: D 302 PHE cc_start: 0.8570 (t80) cc_final: 0.7998 (t80) REVERT: D 303 ILE cc_start: 0.9574 (mp) cc_final: 0.9263 (tp) REVERT: D 315 LYS cc_start: 0.7366 (tptt) cc_final: 0.7142 (tppt) REVERT: D 319 GLU cc_start: 0.9513 (pp20) cc_final: 0.9269 (pp20) REVERT: D 366 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8003 (mp0) REVERT: D 386 LYS cc_start: 0.9331 (ptmt) cc_final: 0.9051 (ptmt) REVERT: D 388 MET cc_start: 0.8923 (mpp) cc_final: 0.8447 (mpp) REVERT: D 404 HIS cc_start: 0.8444 (p-80) cc_final: 0.8194 (p-80) REVERT: D 508 MET cc_start: 0.2072 (ptt) cc_final: 0.1162 (ptt) REVERT: D 516 PHE cc_start: 0.8636 (m-80) cc_final: 0.8377 (m-10) REVERT: D 550 MET cc_start: 0.6039 (pmm) cc_final: 0.5816 (pmm) REVERT: D 562 ILE cc_start: 0.9274 (tp) cc_final: 0.9002 (pt) REVERT: D 575 PHE cc_start: 0.8608 (t80) cc_final: 0.7763 (t80) REVERT: D 609 ASP cc_start: 0.8894 (p0) cc_final: 0.8673 (p0) REVERT: D 687 LEU cc_start: 0.9580 (mt) cc_final: 0.9375 (mt) REVERT: E 218 GLU cc_start: 0.9328 (tt0) cc_final: 0.9054 (tm-30) REVERT: E 219 MET cc_start: 0.9171 (ppp) cc_final: 0.8533 (ppp) REVERT: E 244 TYR cc_start: 0.8324 (p90) cc_final: 0.8108 (p90) REVERT: E 275 MET cc_start: 0.9283 (mpp) cc_final: 0.9061 (mpp) REVERT: E 291 GLU cc_start: 0.9441 (mp0) cc_final: 0.8567 (tp30) REVERT: E 388 MET cc_start: 0.8764 (mmp) cc_final: 0.8243 (mmm) REVERT: E 449 MET cc_start: 0.9076 (mmp) cc_final: 0.8657 (mmp) REVERT: E 451 ASP cc_start: 0.8304 (m-30) cc_final: 0.8092 (m-30) REVERT: E 452 PHE cc_start: 0.7632 (m-80) cc_final: 0.7266 (m-80) REVERT: E 470 GLU cc_start: 0.8563 (tt0) cc_final: 0.7574 (tm-30) REVERT: E 515 LEU cc_start: 0.9154 (mm) cc_final: 0.8941 (mm) REVERT: E 517 TYR cc_start: 0.7795 (p90) cc_final: 0.7477 (p90) REVERT: E 538 ASN cc_start: 0.9064 (t0) cc_final: 0.8437 (m110) REVERT: E 550 MET cc_start: 0.3892 (mmm) cc_final: 0.2477 (tpp) REVERT: E 560 ARG cc_start: 0.9517 (ttt-90) cc_final: 0.9090 (tpp-160) REVERT: E 563 PHE cc_start: 0.9180 (m-10) cc_final: 0.8754 (m-80) REVERT: E 564 ASP cc_start: 0.9205 (m-30) cc_final: 0.8553 (m-30) REVERT: E 572 CYS cc_start: 0.7135 (p) cc_final: 0.6849 (p) REVERT: E 736 PHE cc_start: 0.8831 (m-10) cc_final: 0.8425 (m-10) REVERT: E 740 MET cc_start: 0.8310 (mmp) cc_final: 0.7985 (mmp) REVERT: A 64 ARG cc_start: 0.8689 (tpt90) cc_final: 0.8146 (tpm170) REVERT: A 113 ARG cc_start: 0.8192 (tpm170) cc_final: 0.7946 (tpm170) REVERT: A 135 LEU cc_start: 0.9156 (tp) cc_final: 0.8953 (tp) REVERT: A 163 PHE cc_start: 0.8753 (m-10) cc_final: 0.7896 (m-80) REVERT: A 241 ILE cc_start: 0.8733 (tp) cc_final: 0.8068 (tp) REVERT: A 243 LEU cc_start: 0.9277 (mm) cc_final: 0.8973 (mm) REVERT: A 253 LEU cc_start: 0.9398 (mt) cc_final: 0.8827 (mp) REVERT: A 275 MET cc_start: 0.9501 (mtm) cc_final: 0.9296 (mtt) REVERT: A 344 MET cc_start: 0.8578 (mmp) cc_final: 0.7793 (mmp) REVERT: A 366 GLU cc_start: 0.7671 (tt0) cc_final: 0.7401 (tt0) REVERT: A 388 MET cc_start: 0.7892 (mpp) cc_final: 0.7565 (mpp) REVERT: A 417 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 516 PHE cc_start: 0.8982 (m-80) cc_final: 0.8052 (m-80) REVERT: A 651 LYS cc_start: 0.9444 (pttt) cc_final: 0.9046 (tmtt) REVERT: F 204 ASP cc_start: 0.8845 (m-30) cc_final: 0.8138 (p0) REVERT: F 222 LEU cc_start: 0.9472 (tp) cc_final: 0.8578 (tp) REVERT: F 253 LEU cc_start: 0.9739 (mm) cc_final: 0.9487 (mm) REVERT: F 269 ILE cc_start: 0.9610 (mt) cc_final: 0.9087 (mt) REVERT: F 270 ASN cc_start: 0.9445 (t0) cc_final: 0.9038 (t0) REVERT: F 337 GLN cc_start: 0.7178 (mm110) cc_final: 0.5065 (tp40) REVERT: F 351 ASN cc_start: 0.9038 (p0) cc_final: 0.8759 (p0) REVERT: F 368 ASP cc_start: 0.8871 (t0) cc_final: 0.8668 (t0) REVERT: F 442 MET cc_start: 0.8471 (mmp) cc_final: 0.7348 (ptt) REVERT: F 470 GLU cc_start: 0.7968 (pp20) cc_final: 0.7328 (pm20) REVERT: F 495 TYR cc_start: 0.8875 (m-80) cc_final: 0.8279 (m-80) REVERT: F 517 TYR cc_start: 0.9389 (p90) cc_final: 0.9133 (p90) REVERT: F 565 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8991 (ptmt) REVERT: F 608 MET cc_start: 0.8051 (ptp) cc_final: 0.7851 (ptm) REVERT: F 609 ASP cc_start: 0.9114 (m-30) cc_final: 0.8770 (m-30) REVERT: F 611 MET cc_start: 0.7889 (pmm) cc_final: 0.7257 (pmm) REVERT: F 678 MET cc_start: 0.8401 (tpt) cc_final: 0.8074 (mtp) REVERT: F 682 PHE cc_start: 0.7741 (m-10) cc_final: 0.7498 (m-10) REVERT: F 740 MET cc_start: 0.4445 (pmm) cc_final: 0.3939 (pmm) outliers start: 2 outliers final: 0 residues processed: 761 average time/residue: 0.4660 time to fit residues: 546.6683 Evaluate side-chains 571 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 570 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 190 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 chunk 389 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 285 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 624 ASN F 641 GLN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 32516 Z= 0.483 Angle : 0.974 12.351 43942 Z= 0.507 Chirality : 0.053 0.219 4978 Planarity : 0.008 0.110 5767 Dihedral : 8.718 173.128 4446 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 46.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.12 % Favored : 90.86 % Rotamer: Outliers : 0.20 % Allowed : 8.01 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.12), residues: 4015 helix: -1.87 (0.11), residues: 1644 sheet: -1.79 (0.22), residues: 516 loop : -1.62 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 551 HIS 0.035 0.004 HIS E 384 PHE 0.030 0.004 PHE A 290 TYR 0.022 0.003 TYR E 495 ARG 0.012 0.001 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 671 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8622 (mmp) cc_final: 0.8332 (mmm) REVERT: B 81 LYS cc_start: 0.9098 (tptt) cc_final: 0.8415 (tppt) REVERT: B 119 ILE cc_start: 0.8378 (pt) cc_final: 0.8175 (tt) REVERT: B 190 LYS cc_start: 0.9249 (tmmt) cc_final: 0.8995 (mmtm) REVERT: B 218 GLU cc_start: 0.9016 (pm20) cc_final: 0.8792 (pm20) REVERT: B 275 MET cc_start: 0.9566 (mpp) cc_final: 0.8904 (mpp) REVERT: B 305 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8279 (mm-30) REVERT: B 366 GLU cc_start: 0.9159 (pm20) cc_final: 0.8704 (pm20) REVERT: B 388 MET cc_start: 0.8635 (mmp) cc_final: 0.7746 (mmm) REVERT: B 517 TYR cc_start: 0.8841 (p90) cc_final: 0.8553 (p90) REVERT: B 538 ASN cc_start: 0.9216 (t0) cc_final: 0.8736 (t0) REVERT: B 565 LYS cc_start: 0.9635 (pptt) cc_final: 0.9368 (pptt) REVERT: B 678 MET cc_start: 0.7832 (mtt) cc_final: 0.7091 (ptt) REVERT: B 757 MET cc_start: 0.8598 (ttt) cc_final: 0.8368 (tmm) REVERT: C 59 LEU cc_start: 0.8127 (tt) cc_final: 0.7789 (tt) REVERT: C 190 LYS cc_start: 0.9720 (pptt) cc_final: 0.9402 (pptt) REVERT: C 221 GLU cc_start: 0.8310 (pt0) cc_final: 0.8041 (pt0) REVERT: C 244 TYR cc_start: 0.7139 (p90) cc_final: 0.6863 (p90) REVERT: C 269 ILE cc_start: 0.9401 (mp) cc_final: 0.9174 (mp) REVERT: C 291 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9094 (mt-10) REVERT: C 306 LEU cc_start: 0.9351 (mm) cc_final: 0.9116 (mm) REVERT: C 340 HIS cc_start: 0.7745 (m90) cc_final: 0.7439 (m90) REVERT: C 357 LEU cc_start: 0.9692 (mm) cc_final: 0.9452 (mm) REVERT: C 362 ARG cc_start: 0.8459 (mpp-170) cc_final: 0.8114 (mpt180) REVERT: C 449 MET cc_start: 0.8904 (mmp) cc_final: 0.8223 (mmm) REVERT: C 563 PHE cc_start: 0.9313 (m-80) cc_final: 0.8983 (m-80) REVERT: C 639 LEU cc_start: 0.6966 (mm) cc_final: 0.6688 (mm) REVERT: C 662 ARG cc_start: 0.9045 (tmm160) cc_final: 0.8725 (tmm160) REVERT: C 696 LYS cc_start: 0.9740 (tppt) cc_final: 0.9308 (tppt) REVERT: D 158 MET cc_start: 0.7912 (ppp) cc_final: 0.7049 (ppp) REVERT: D 199 ASN cc_start: 0.8625 (p0) cc_final: 0.8417 (p0) REVERT: D 219 MET cc_start: 0.8823 (pmm) cc_final: 0.8388 (pmm) REVERT: D 242 LEU cc_start: 0.9499 (mm) cc_final: 0.9274 (mm) REVERT: D 268 LEU cc_start: 0.9303 (tt) cc_final: 0.8851 (tt) REVERT: D 269 ILE cc_start: 0.9534 (mt) cc_final: 0.9329 (mt) REVERT: D 273 GLU cc_start: 0.8804 (mp0) cc_final: 0.8204 (mp0) REVERT: D 288 LYS cc_start: 0.9368 (pptt) cc_final: 0.9141 (pptt) REVERT: D 301 ILE cc_start: 0.9366 (mp) cc_final: 0.8990 (mp) REVERT: D 302 PHE cc_start: 0.8505 (t80) cc_final: 0.8159 (t80) REVERT: D 315 LYS cc_start: 0.7485 (tptt) cc_final: 0.7184 (tppt) REVERT: D 344 MET cc_start: 0.8815 (ppp) cc_final: 0.8540 (ppp) REVERT: D 388 MET cc_start: 0.8937 (mpp) cc_final: 0.8610 (mpp) REVERT: D 414 LEU cc_start: 0.9039 (tt) cc_final: 0.8761 (tt) REVERT: D 449 MET cc_start: 0.8908 (mmp) cc_final: 0.8583 (mmp) REVERT: D 508 MET cc_start: 0.3289 (ptt) cc_final: 0.2091 (ptt) REVERT: D 516 PHE cc_start: 0.8770 (m-80) cc_final: 0.8508 (m-10) REVERT: D 550 MET cc_start: 0.6416 (pmm) cc_final: 0.6081 (pmm) REVERT: D 562 ILE cc_start: 0.9450 (tp) cc_final: 0.9173 (pt) REVERT: D 575 PHE cc_start: 0.8662 (t80) cc_final: 0.8227 (t80) REVERT: E 218 GLU cc_start: 0.9470 (tt0) cc_final: 0.9057 (tm-30) REVERT: E 219 MET cc_start: 0.9326 (ppp) cc_final: 0.8972 (ppp) REVERT: E 275 MET cc_start: 0.9451 (mpp) cc_final: 0.9147 (mpp) REVERT: E 291 GLU cc_start: 0.9458 (mp0) cc_final: 0.9255 (pt0) REVERT: E 379 GLU cc_start: 0.9069 (tp30) cc_final: 0.8812 (tp30) REVERT: E 383 ILE cc_start: 0.9653 (mt) cc_final: 0.9445 (mt) REVERT: E 388 MET cc_start: 0.8819 (mmp) cc_final: 0.8399 (mmm) REVERT: E 470 GLU cc_start: 0.8946 (tt0) cc_final: 0.7868 (tm-30) REVERT: E 515 LEU cc_start: 0.9216 (mm) cc_final: 0.8951 (mm) REVERT: E 517 TYR cc_start: 0.7802 (p90) cc_final: 0.7089 (p90) REVERT: E 538 ASN cc_start: 0.9133 (t0) cc_final: 0.8532 (m110) REVERT: E 550 MET cc_start: 0.3508 (mmm) cc_final: 0.2644 (tpp) REVERT: E 563 PHE cc_start: 0.9250 (m-10) cc_final: 0.8831 (m-80) REVERT: E 572 CYS cc_start: 0.7639 (p) cc_final: 0.7188 (p) REVERT: E 635 ARG cc_start: 0.9053 (ptt-90) cc_final: 0.8382 (ptm160) REVERT: E 639 LEU cc_start: 0.9225 (pp) cc_final: 0.8803 (pp) REVERT: E 736 PHE cc_start: 0.9003 (m-80) cc_final: 0.8573 (m-10) REVERT: E 741 ARG cc_start: 0.8969 (tpm170) cc_final: 0.8314 (ttp80) REVERT: A 135 LEU cc_start: 0.9145 (tp) cc_final: 0.8863 (tp) REVERT: A 275 MET cc_start: 0.9629 (mtm) cc_final: 0.9354 (mtt) REVERT: A 306 LEU cc_start: 0.8570 (tp) cc_final: 0.8191 (tp) REVERT: A 349 ARG cc_start: 0.9472 (mmm-85) cc_final: 0.9255 (mmm-85) REVERT: A 360 PHE cc_start: 0.8745 (t80) cc_final: 0.8316 (t80) REVERT: A 388 MET cc_start: 0.8752 (mpp) cc_final: 0.8357 (mpp) REVERT: A 516 PHE cc_start: 0.8916 (m-80) cc_final: 0.8132 (m-80) REVERT: A 561 GLU cc_start: 0.9226 (tt0) cc_final: 0.8620 (tm-30) REVERT: A 651 LYS cc_start: 0.9451 (pttt) cc_final: 0.9065 (tmtt) REVERT: F 204 ASP cc_start: 0.9209 (m-30) cc_final: 0.8610 (p0) REVERT: F 222 LEU cc_start: 0.9489 (tp) cc_final: 0.9042 (tp) REVERT: F 253 LEU cc_start: 0.9750 (mm) cc_final: 0.9545 (mm) REVERT: F 269 ILE cc_start: 0.9718 (mt) cc_final: 0.9501 (tp) REVERT: F 288 LYS cc_start: 0.9212 (ptpp) cc_final: 0.8956 (pttm) REVERT: F 329 LEU cc_start: 0.9317 (mt) cc_final: 0.9051 (mm) REVERT: F 414 LEU cc_start: 0.9565 (tp) cc_final: 0.9338 (mm) REVERT: F 417 GLU cc_start: 0.9480 (mp0) cc_final: 0.9149 (mp0) REVERT: F 470 GLU cc_start: 0.8551 (pp20) cc_final: 0.8228 (pt0) REVERT: F 508 MET cc_start: 0.0321 (ttt) cc_final: -0.0723 (tmm) REVERT: F 565 LYS cc_start: 0.9334 (ptmm) cc_final: 0.8812 (pttp) REVERT: F 571 PRO cc_start: 0.7869 (Cg_endo) cc_final: 0.7623 (Cg_exo) REVERT: F 608 MET cc_start: 0.8278 (ptp) cc_final: 0.8026 (ptp) REVERT: F 609 ASP cc_start: 0.9098 (m-30) cc_final: 0.8625 (m-30) REVERT: F 611 MET cc_start: 0.7922 (pmm) cc_final: 0.7128 (pmm) outliers start: 7 outliers final: 3 residues processed: 678 average time/residue: 0.4853 time to fit residues: 505.2975 Evaluate side-chains 501 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 498 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 chunk 160 optimal weight: 0.2980 chunk 332 optimal weight: 0.8980 chunk 269 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 349 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 568 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32516 Z= 0.222 Angle : 0.761 9.840 43942 Z= 0.378 Chirality : 0.049 0.244 4978 Planarity : 0.006 0.105 5767 Dihedral : 8.290 178.360 4446 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 4015 helix: -1.42 (0.12), residues: 1647 sheet: -1.48 (0.23), residues: 469 loop : -1.38 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 476 HIS 0.012 0.002 HIS A 735 PHE 0.033 0.002 PHE B 563 TYR 0.032 0.002 TYR A 495 ARG 0.014 0.001 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 713 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8446 (mmp) cc_final: 0.8171 (mmm) REVERT: B 84 MET cc_start: 0.9093 (mmp) cc_final: 0.8721 (mmm) REVERT: B 130 LEU cc_start: 0.8538 (tt) cc_final: 0.7409 (mp) REVERT: B 143 TYR cc_start: 0.9450 (m-80) cc_final: 0.9181 (m-80) REVERT: B 275 MET cc_start: 0.9525 (mpp) cc_final: 0.8828 (mpp) REVERT: B 302 PHE cc_start: 0.8475 (t80) cc_final: 0.7985 (t80) REVERT: B 305 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 359 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7970 (ttp80) REVERT: B 363 PHE cc_start: 0.8271 (m-10) cc_final: 0.7923 (m-10) REVERT: B 388 MET cc_start: 0.8405 (mmp) cc_final: 0.7525 (mmm) REVERT: B 426 LYS cc_start: 0.9629 (mptt) cc_final: 0.9369 (mmtt) REVERT: B 514 VAL cc_start: 0.8456 (p) cc_final: 0.8040 (p) REVERT: B 517 TYR cc_start: 0.8560 (p90) cc_final: 0.8225 (p90) REVERT: B 538 ASN cc_start: 0.9198 (t0) cc_final: 0.8797 (t0) REVERT: B 620 ILE cc_start: 0.9330 (mp) cc_final: 0.8958 (mp) REVERT: B 678 MET cc_start: 0.7787 (mtt) cc_final: 0.7030 (ptt) REVERT: B 757 MET cc_start: 0.8528 (ttt) cc_final: 0.8285 (tmm) REVERT: C 59 LEU cc_start: 0.8253 (tt) cc_final: 0.7975 (tt) REVERT: C 117 LEU cc_start: 0.8400 (mt) cc_final: 0.7958 (mt) REVERT: C 163 PHE cc_start: 0.8688 (m-80) cc_final: 0.8178 (m-80) REVERT: C 190 LYS cc_start: 0.9689 (pptt) cc_final: 0.9373 (pptt) REVERT: C 201 VAL cc_start: 0.8904 (m) cc_final: 0.8374 (p) REVERT: C 203 TYR cc_start: 0.8682 (m-80) cc_final: 0.7384 (m-80) REVERT: C 221 GLU cc_start: 0.8315 (pt0) cc_final: 0.8005 (pp20) REVERT: C 244 TYR cc_start: 0.7237 (p90) cc_final: 0.6730 (p90) REVERT: C 261 GLU cc_start: 0.7842 (pt0) cc_final: 0.5820 (pt0) REVERT: C 265 PHE cc_start: 0.8062 (t80) cc_final: 0.7820 (t80) REVERT: C 269 ILE cc_start: 0.9364 (mp) cc_final: 0.9003 (mp) REVERT: C 291 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8941 (mt-10) REVERT: C 357 LEU cc_start: 0.9635 (mm) cc_final: 0.9406 (mm) REVERT: C 368 ASP cc_start: 0.7639 (p0) cc_final: 0.7348 (p0) REVERT: C 369 ILE cc_start: 0.8756 (mp) cc_final: 0.8525 (tp) REVERT: C 388 MET cc_start: 0.8427 (pmm) cc_final: 0.8055 (pmm) REVERT: C 417 GLU cc_start: 0.9348 (tp30) cc_final: 0.9040 (tp30) REVERT: C 423 ILE cc_start: 0.9572 (mt) cc_final: 0.9296 (mm) REVERT: C 442 MET cc_start: 0.9168 (mmp) cc_final: 0.8850 (tpp) REVERT: C 449 MET cc_start: 0.8777 (mmp) cc_final: 0.8014 (mmm) REVERT: C 515 LEU cc_start: 0.8846 (mm) cc_final: 0.8599 (mm) REVERT: C 609 ASP cc_start: 0.9372 (m-30) cc_final: 0.8733 (m-30) REVERT: C 639 LEU cc_start: 0.6611 (mm) cc_final: 0.6304 (mm) REVERT: C 696 LYS cc_start: 0.9730 (tppt) cc_final: 0.9253 (mmmt) REVERT: D 135 LEU cc_start: 0.8454 (mt) cc_final: 0.8103 (mt) REVERT: D 139 PHE cc_start: 0.9028 (m-80) cc_final: 0.8719 (m-80) REVERT: D 158 MET cc_start: 0.7711 (ppp) cc_final: 0.6884 (ppp) REVERT: D 199 ASN cc_start: 0.8683 (p0) cc_final: 0.8363 (p0) REVERT: D 219 MET cc_start: 0.8475 (pmm) cc_final: 0.7950 (pmm) REVERT: D 242 LEU cc_start: 0.9571 (mm) cc_final: 0.9210 (mm) REVERT: D 268 LEU cc_start: 0.9265 (tt) cc_final: 0.8770 (tt) REVERT: D 301 ILE cc_start: 0.9267 (mp) cc_final: 0.8967 (mp) REVERT: D 302 PHE cc_start: 0.8529 (t80) cc_final: 0.8144 (t80) REVERT: D 315 LYS cc_start: 0.7472 (tptt) cc_final: 0.7172 (tppt) REVERT: D 319 GLU cc_start: 0.9565 (pp20) cc_final: 0.9289 (pp20) REVERT: D 344 MET cc_start: 0.8667 (ppp) cc_final: 0.8457 (ppp) REVERT: D 366 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8114 (mm-30) REVERT: D 383 ILE cc_start: 0.9211 (pt) cc_final: 0.8874 (pt) REVERT: D 386 LYS cc_start: 0.9330 (ptmt) cc_final: 0.8918 (ptmm) REVERT: D 388 MET cc_start: 0.9054 (mpp) cc_final: 0.8604 (mpp) REVERT: D 397 GLU cc_start: 0.8719 (mp0) cc_final: 0.8445 (mp0) REVERT: D 410 ASP cc_start: 0.9126 (p0) cc_final: 0.8851 (p0) REVERT: D 414 LEU cc_start: 0.8892 (tt) cc_final: 0.8536 (tt) REVERT: D 516 PHE cc_start: 0.8517 (m-80) cc_final: 0.8301 (m-10) REVERT: D 550 MET cc_start: 0.6964 (pmm) cc_final: 0.6759 (pmm) REVERT: D 562 ILE cc_start: 0.9422 (tp) cc_final: 0.9136 (pt) REVERT: D 575 PHE cc_start: 0.8582 (t80) cc_final: 0.8152 (t80) REVERT: D 639 LEU cc_start: 0.7412 (mp) cc_final: 0.7206 (mp) REVERT: E 218 GLU cc_start: 0.9450 (tt0) cc_final: 0.9022 (tm-30) REVERT: E 219 MET cc_start: 0.9286 (ppp) cc_final: 0.8952 (ppp) REVERT: E 275 MET cc_start: 0.9431 (mpp) cc_final: 0.9111 (mpp) REVERT: E 379 GLU cc_start: 0.8940 (tp30) cc_final: 0.8704 (tp30) REVERT: E 388 MET cc_start: 0.8844 (mmp) cc_final: 0.8360 (mmm) REVERT: E 452 PHE cc_start: 0.8388 (m-80) cc_final: 0.7989 (m-80) REVERT: E 470 GLU cc_start: 0.8262 (tt0) cc_final: 0.7366 (tm-30) REVERT: E 515 LEU cc_start: 0.9193 (mm) cc_final: 0.8915 (mm) REVERT: E 517 TYR cc_start: 0.7723 (p90) cc_final: 0.7051 (p90) REVERT: E 538 ASN cc_start: 0.8919 (t0) cc_final: 0.8323 (m110) REVERT: E 550 MET cc_start: 0.4028 (mmm) cc_final: 0.3152 (tpp) REVERT: E 563 PHE cc_start: 0.9253 (m-10) cc_final: 0.8794 (m-80) REVERT: E 572 CYS cc_start: 0.7832 (p) cc_final: 0.7426 (p) REVERT: E 609 ASP cc_start: 0.7838 (t0) cc_final: 0.7610 (t0) REVERT: E 639 LEU cc_start: 0.9144 (pp) cc_final: 0.8748 (pp) REVERT: E 736 PHE cc_start: 0.8974 (m-80) cc_final: 0.8639 (m-10) REVERT: E 741 ARG cc_start: 0.8964 (tpm170) cc_final: 0.8477 (mmt-90) REVERT: A 50 GLN cc_start: 0.9290 (pp30) cc_final: 0.8959 (pp30) REVERT: A 64 ARG cc_start: 0.8483 (tpt90) cc_final: 0.8018 (mmm160) REVERT: A 253 LEU cc_start: 0.9511 (mp) cc_final: 0.9145 (mp) REVERT: A 256 ARG cc_start: 0.8772 (mtm-85) cc_final: 0.8413 (mtm-85) REVERT: A 349 ARG cc_start: 0.9413 (mmm-85) cc_final: 0.9157 (mmm-85) REVERT: A 388 MET cc_start: 0.8172 (mpp) cc_final: 0.7599 (mpp) REVERT: A 516 PHE cc_start: 0.8885 (m-80) cc_final: 0.7950 (m-80) REVERT: A 561 GLU cc_start: 0.9189 (tt0) cc_final: 0.8504 (tm-30) REVERT: A 651 LYS cc_start: 0.9444 (pttt) cc_final: 0.9041 (tmtt) REVERT: A 661 LEU cc_start: 0.7962 (pp) cc_final: 0.7372 (pp) REVERT: F 204 ASP cc_start: 0.9059 (m-30) cc_final: 0.8249 (p0) REVERT: F 222 LEU cc_start: 0.9415 (tp) cc_final: 0.9054 (tp) REVERT: F 242 LEU cc_start: 0.9297 (mt) cc_final: 0.8899 (mt) REVERT: F 253 LEU cc_start: 0.9732 (mm) cc_final: 0.9523 (mm) REVERT: F 269 ILE cc_start: 0.9605 (mt) cc_final: 0.9170 (mt) REVERT: F 270 ASN cc_start: 0.9314 (t0) cc_final: 0.8947 (t0) REVERT: F 288 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8896 (ptpt) REVERT: F 337 GLN cc_start: 0.6894 (mm-40) cc_final: 0.6689 (tp40) REVERT: F 417 GLU cc_start: 0.9482 (mp0) cc_final: 0.9108 (mp0) REVERT: F 442 MET cc_start: 0.8607 (mmp) cc_final: 0.7487 (ptt) REVERT: F 470 GLU cc_start: 0.8467 (pp20) cc_final: 0.7325 (pm20) REVERT: F 560 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7663 (mmm-85) REVERT: F 609 ASP cc_start: 0.9073 (m-30) cc_final: 0.8730 (m-30) REVERT: F 611 MET cc_start: 0.8175 (pmm) cc_final: 0.7722 (pmm) REVERT: F 678 MET cc_start: 0.8477 (tpt) cc_final: 0.8224 (mmt) REVERT: F 682 PHE cc_start: 0.7893 (m-10) cc_final: 0.7680 (m-80) outliers start: 1 outliers final: 0 residues processed: 714 average time/residue: 0.4741 time to fit residues: 524.9885 Evaluate side-chains 550 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 9.9990 chunk 350 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 128 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 458 GLN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN E 460 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 692 GLN ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32516 Z= 0.198 Angle : 0.741 10.269 43942 Z= 0.367 Chirality : 0.049 0.276 4978 Planarity : 0.005 0.078 5767 Dihedral : 7.920 175.552 4446 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.00 % Favored : 91.98 % Rotamer: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 4015 helix: -1.21 (0.12), residues: 1651 sheet: -1.40 (0.23), residues: 478 loop : -1.32 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 476 HIS 0.010 0.001 HIS A 735 PHE 0.039 0.002 PHE A 563 TYR 0.017 0.002 TYR E 203 ARG 0.008 0.001 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 712 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8533 (mmp) cc_final: 0.8175 (mmm) REVERT: B 84 MET cc_start: 0.9113 (mmp) cc_final: 0.8624 (mmm) REVERT: B 130 LEU cc_start: 0.8635 (tt) cc_final: 0.7833 (mp) REVERT: B 143 TYR cc_start: 0.9411 (m-80) cc_final: 0.9012 (m-80) REVERT: B 209 CYS cc_start: 0.8228 (m) cc_final: 0.7653 (m) REVERT: B 217 LYS cc_start: 0.9508 (ttpp) cc_final: 0.9245 (tmtt) REVERT: B 218 GLU cc_start: 0.8593 (pm20) cc_final: 0.8339 (pm20) REVERT: B 244 TYR cc_start: 0.8591 (p90) cc_final: 0.8365 (p90) REVERT: B 275 MET cc_start: 0.9519 (mpp) cc_final: 0.8807 (mpp) REVERT: B 302 PHE cc_start: 0.8584 (t80) cc_final: 0.8190 (t80) REVERT: B 305 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8259 (mm-30) REVERT: B 363 PHE cc_start: 0.8101 (m-10) cc_final: 0.7846 (m-80) REVERT: B 366 GLU cc_start: 0.8665 (pm20) cc_final: 0.8352 (pm20) REVERT: B 379 GLU cc_start: 0.9084 (tp30) cc_final: 0.8053 (tt0) REVERT: B 388 MET cc_start: 0.8178 (mmp) cc_final: 0.7105 (mmm) REVERT: B 426 LYS cc_start: 0.9605 (mptt) cc_final: 0.9339 (mmtt) REVERT: B 514 VAL cc_start: 0.8595 (p) cc_final: 0.8050 (p) REVERT: B 515 LEU cc_start: 0.9310 (mm) cc_final: 0.9104 (mm) REVERT: B 517 TYR cc_start: 0.8529 (p90) cc_final: 0.8143 (p90) REVERT: B 538 ASN cc_start: 0.9162 (t0) cc_final: 0.8822 (t0) REVERT: B 565 LYS cc_start: 0.9647 (pptt) cc_final: 0.9390 (pptt) REVERT: B 620 ILE cc_start: 0.9332 (mp) cc_final: 0.9110 (mp) REVERT: B 674 PHE cc_start: 0.9147 (m-80) cc_final: 0.8783 (m-10) REVERT: B 678 MET cc_start: 0.7596 (mtt) cc_final: 0.6899 (ptt) REVERT: B 757 MET cc_start: 0.8446 (ttt) cc_final: 0.8183 (tmm) REVERT: C 59 LEU cc_start: 0.8271 (tt) cc_final: 0.7972 (tt) REVERT: C 163 PHE cc_start: 0.8702 (m-80) cc_final: 0.8116 (m-80) REVERT: C 190 LYS cc_start: 0.9669 (pptt) cc_final: 0.9360 (pptt) REVERT: C 203 TYR cc_start: 0.8628 (m-80) cc_final: 0.7255 (m-10) REVERT: C 221 GLU cc_start: 0.8361 (pt0) cc_final: 0.7941 (pp20) REVERT: C 244 TYR cc_start: 0.7134 (p90) cc_final: 0.5652 (p90) REVERT: C 261 GLU cc_start: 0.7703 (pt0) cc_final: 0.5439 (pt0) REVERT: C 265 PHE cc_start: 0.8158 (t80) cc_final: 0.7937 (t80) REVERT: C 269 ILE cc_start: 0.9360 (mp) cc_final: 0.9013 (mp) REVERT: C 285 ASN cc_start: 0.8903 (t160) cc_final: 0.8219 (t0) REVERT: C 288 LYS cc_start: 0.9302 (tttt) cc_final: 0.9057 (pttp) REVERT: C 291 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8906 (mt-10) REVERT: C 369 ILE cc_start: 0.8781 (mp) cc_final: 0.8523 (tp) REVERT: C 388 MET cc_start: 0.8319 (pmm) cc_final: 0.8020 (pmm) REVERT: C 417 GLU cc_start: 0.9285 (tp30) cc_final: 0.9031 (tp30) REVERT: C 423 ILE cc_start: 0.9539 (mt) cc_final: 0.9260 (mm) REVERT: C 442 MET cc_start: 0.9152 (mmp) cc_final: 0.8817 (tpp) REVERT: C 449 MET cc_start: 0.8643 (mmp) cc_final: 0.7848 (mmm) REVERT: C 515 LEU cc_start: 0.8840 (mm) cc_final: 0.8606 (mm) REVERT: C 609 ASP cc_start: 0.9408 (m-30) cc_final: 0.8779 (m-30) REVERT: C 639 LEU cc_start: 0.6618 (mm) cc_final: 0.6329 (mm) REVERT: C 696 LYS cc_start: 0.9753 (tppt) cc_final: 0.9235 (mmmt) REVERT: D 135 LEU cc_start: 0.8471 (mt) cc_final: 0.8109 (mt) REVERT: D 139 PHE cc_start: 0.9008 (m-80) cc_final: 0.8667 (m-80) REVERT: D 158 MET cc_start: 0.7481 (ppp) cc_final: 0.6844 (ppp) REVERT: D 164 LYS cc_start: 0.7190 (tppt) cc_final: 0.6507 (tppt) REVERT: D 199 ASN cc_start: 0.8788 (p0) cc_final: 0.8355 (p0) REVERT: D 219 MET cc_start: 0.8475 (pmm) cc_final: 0.8001 (pmm) REVERT: D 268 LEU cc_start: 0.9333 (tt) cc_final: 0.8706 (tt) REVERT: D 273 GLU cc_start: 0.8545 (mp0) cc_final: 0.7914 (mp0) REVERT: D 302 PHE cc_start: 0.8566 (t80) cc_final: 0.8352 (t80) REVERT: D 315 LYS cc_start: 0.7350 (tptt) cc_final: 0.7137 (tptt) REVERT: D 319 GLU cc_start: 0.9554 (pp20) cc_final: 0.9204 (pp20) REVERT: D 366 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8079 (mp0) REVERT: D 382 GLN cc_start: 0.9120 (pt0) cc_final: 0.8784 (pt0) REVERT: D 386 LYS cc_start: 0.9220 (ptmt) cc_final: 0.8916 (ptmm) REVERT: D 388 MET cc_start: 0.9005 (mpp) cc_final: 0.8618 (mpp) REVERT: D 410 ASP cc_start: 0.8975 (p0) cc_final: 0.8730 (p0) REVERT: D 449 MET cc_start: 0.8912 (mmp) cc_final: 0.8620 (mmp) REVERT: D 516 PHE cc_start: 0.8499 (m-80) cc_final: 0.8275 (m-10) REVERT: D 562 ILE cc_start: 0.9366 (tp) cc_final: 0.9142 (pt) REVERT: D 574 LEU cc_start: 0.9540 (tp) cc_final: 0.9311 (tp) REVERT: D 575 PHE cc_start: 0.8553 (t80) cc_final: 0.8218 (t80) REVERT: E 218 GLU cc_start: 0.9439 (tt0) cc_final: 0.9031 (tm-30) REVERT: E 219 MET cc_start: 0.9295 (ppp) cc_final: 0.9022 (ppp) REVERT: E 267 PHE cc_start: 0.8650 (t80) cc_final: 0.8353 (t80) REVERT: E 275 MET cc_start: 0.9316 (mpp) cc_final: 0.9058 (mpp) REVERT: E 338 ARG cc_start: 0.8500 (mmt90) cc_final: 0.7890 (tpt90) REVERT: E 348 ASN cc_start: 0.9230 (m-40) cc_final: 0.8916 (p0) REVERT: E 379 GLU cc_start: 0.9050 (tp30) cc_final: 0.8736 (tp30) REVERT: E 388 MET cc_start: 0.8773 (mmp) cc_final: 0.8329 (mmm) REVERT: E 452 PHE cc_start: 0.8430 (m-80) cc_final: 0.8116 (m-80) REVERT: E 515 LEU cc_start: 0.9176 (mm) cc_final: 0.8884 (mm) REVERT: E 517 TYR cc_start: 0.7628 (p90) cc_final: 0.6984 (p90) REVERT: E 538 ASN cc_start: 0.9028 (t0) cc_final: 0.8375 (m110) REVERT: E 542 ILE cc_start: 0.9518 (tp) cc_final: 0.9316 (tp) REVERT: E 550 MET cc_start: 0.3924 (mmm) cc_final: 0.3147 (tpp) REVERT: E 563 PHE cc_start: 0.9267 (m-10) cc_final: 0.8952 (m-80) REVERT: E 567 ARG cc_start: 0.8671 (ptp-170) cc_final: 0.8142 (ttp80) REVERT: E 572 CYS cc_start: 0.7610 (p) cc_final: 0.7216 (p) REVERT: E 639 LEU cc_start: 0.9132 (pp) cc_final: 0.8664 (pp) REVERT: E 736 PHE cc_start: 0.8954 (m-80) cc_final: 0.8612 (m-10) REVERT: E 740 MET cc_start: 0.8078 (mmp) cc_final: 0.6862 (mmp) REVERT: E 741 ARG cc_start: 0.8991 (tpm170) cc_final: 0.8533 (mmt180) REVERT: A 50 GLN cc_start: 0.9353 (pp30) cc_final: 0.9084 (pp30) REVERT: A 64 ARG cc_start: 0.8635 (tpt90) cc_final: 0.8016 (mmm160) REVERT: A 84 MET cc_start: 0.9076 (mpp) cc_final: 0.8767 (mpp) REVERT: A 135 LEU cc_start: 0.9135 (tp) cc_final: 0.8918 (tp) REVERT: A 163 PHE cc_start: 0.8731 (m-80) cc_final: 0.7904 (m-80) REVERT: A 253 LEU cc_start: 0.9483 (mp) cc_final: 0.9206 (mp) REVERT: A 275 MET cc_start: 0.9486 (mtm) cc_final: 0.9282 (mtt) REVERT: A 349 ARG cc_start: 0.9384 (mmm-85) cc_final: 0.9165 (mmm-85) REVERT: A 366 GLU cc_start: 0.7569 (tt0) cc_final: 0.6981 (tt0) REVERT: A 515 LEU cc_start: 0.9186 (tp) cc_final: 0.8966 (mm) REVERT: A 516 PHE cc_start: 0.8882 (m-80) cc_final: 0.7946 (m-80) REVERT: A 561 GLU cc_start: 0.9138 (tt0) cc_final: 0.8474 (tm-30) REVERT: A 651 LYS cc_start: 0.9439 (pttt) cc_final: 0.9029 (tmtt) REVERT: A 661 LEU cc_start: 0.7862 (pp) cc_final: 0.7360 (pp) REVERT: A 761 THR cc_start: 0.9030 (m) cc_final: 0.8787 (m) REVERT: F 204 ASP cc_start: 0.8912 (m-30) cc_final: 0.8045 (p0) REVERT: F 267 PHE cc_start: 0.8304 (t80) cc_final: 0.8096 (t80) REVERT: F 269 ILE cc_start: 0.9551 (mt) cc_final: 0.9229 (mt) REVERT: F 270 ASN cc_start: 0.9302 (t0) cc_final: 0.8991 (t0) REVERT: F 307 ASP cc_start: 0.7401 (m-30) cc_final: 0.6974 (p0) REVERT: F 348 ASN cc_start: 0.8860 (t0) cc_final: 0.8553 (p0) REVERT: F 417 GLU cc_start: 0.9509 (mp0) cc_final: 0.9080 (mp0) REVERT: F 427 MET cc_start: 0.6760 (tpp) cc_final: 0.6174 (tpp) REVERT: F 442 MET cc_start: 0.8550 (mmp) cc_final: 0.7445 (ptt) REVERT: F 470 GLU cc_start: 0.8383 (pp20) cc_final: 0.7311 (pm20) REVERT: F 495 TYR cc_start: 0.8863 (m-80) cc_final: 0.8468 (m-10) REVERT: F 565 LYS cc_start: 0.9189 (ptmm) cc_final: 0.8788 (pttp) REVERT: F 609 ASP cc_start: 0.9061 (m-30) cc_final: 0.8720 (m-30) REVERT: F 611 MET cc_start: 0.8268 (pmm) cc_final: 0.7879 (pmm) outliers start: 1 outliers final: 0 residues processed: 713 average time/residue: 0.4948 time to fit residues: 556.0657 Evaluate side-chains 556 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 222 optimal weight: 8.9990 chunk 284 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 328 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 236 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32516 Z= 0.349 Angle : 0.846 10.555 43942 Z= 0.433 Chirality : 0.051 0.267 4978 Planarity : 0.007 0.098 5767 Dihedral : 8.151 177.324 4446 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 39.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.13), residues: 4015 helix: -1.51 (0.12), residues: 1646 sheet: -1.68 (0.22), residues: 483 loop : -1.46 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 476 HIS 0.010 0.002 HIS F 735 PHE 0.026 0.003 PHE A 506 TYR 0.032 0.003 TYR A 203 ARG 0.014 0.001 ARG E 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8515 (mmp) cc_final: 0.8248 (mmm) REVERT: B 51 LEU cc_start: 0.8001 (mp) cc_final: 0.7650 (mt) REVERT: B 84 MET cc_start: 0.9121 (mmp) cc_final: 0.8554 (mmm) REVERT: B 130 LEU cc_start: 0.8544 (tt) cc_final: 0.7574 (mp) REVERT: B 275 MET cc_start: 0.9560 (mpp) cc_final: 0.8898 (mpp) REVERT: B 302 PHE cc_start: 0.8727 (t80) cc_final: 0.7365 (t80) REVERT: B 305 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 363 PHE cc_start: 0.8259 (m-10) cc_final: 0.8028 (m-80) REVERT: B 366 GLU cc_start: 0.8920 (pm20) cc_final: 0.8582 (pm20) REVERT: B 386 LYS cc_start: 0.9147 (tppp) cc_final: 0.8932 (tppp) REVERT: B 388 MET cc_start: 0.8387 (mmp) cc_final: 0.7273 (mmm) REVERT: B 508 MET cc_start: 0.4534 (mtp) cc_final: 0.4253 (mtm) REVERT: B 514 VAL cc_start: 0.8101 (p) cc_final: 0.6934 (p) REVERT: B 515 LEU cc_start: 0.9288 (mm) cc_final: 0.8968 (mm) REVERT: B 517 TYR cc_start: 0.8391 (p90) cc_final: 0.7527 (p90) REVERT: B 524 LYS cc_start: 0.9033 (mttt) cc_final: 0.8016 (pttt) REVERT: B 538 ASN cc_start: 0.9247 (t0) cc_final: 0.8851 (t0) REVERT: B 620 ILE cc_start: 0.9392 (mp) cc_final: 0.9170 (mp) REVERT: B 674 PHE cc_start: 0.9234 (m-80) cc_final: 0.8893 (m-10) REVERT: B 678 MET cc_start: 0.7977 (mtt) cc_final: 0.7121 (ptt) REVERT: B 757 MET cc_start: 0.8575 (ttt) cc_final: 0.8339 (tmm) REVERT: C 59 LEU cc_start: 0.8157 (tt) cc_final: 0.7799 (tt) REVERT: C 203 TYR cc_start: 0.8512 (m-80) cc_final: 0.7498 (m-10) REVERT: C 221 GLU cc_start: 0.8366 (pt0) cc_final: 0.8058 (pp20) REVERT: C 244 TYR cc_start: 0.6372 (p90) cc_final: 0.6014 (p90) REVERT: C 333 ASP cc_start: 0.8114 (t0) cc_final: 0.7816 (m-30) REVERT: C 388 MET cc_start: 0.8764 (pmm) cc_final: 0.8501 (pmm) REVERT: C 423 ILE cc_start: 0.9547 (mt) cc_final: 0.9256 (mm) REVERT: C 442 MET cc_start: 0.9122 (mmp) cc_final: 0.8726 (tpp) REVERT: C 449 MET cc_start: 0.8770 (mmp) cc_final: 0.8069 (mmm) REVERT: C 609 ASP cc_start: 0.9329 (m-30) cc_final: 0.8860 (m-30) REVERT: C 639 LEU cc_start: 0.6794 (mm) cc_final: 0.6507 (mm) REVERT: C 696 LYS cc_start: 0.9772 (tppt) cc_final: 0.9325 (mtmm) REVERT: D 158 MET cc_start: 0.8073 (ppp) cc_final: 0.7081 (ppp) REVERT: D 199 ASN cc_start: 0.8696 (p0) cc_final: 0.8305 (p0) REVERT: D 219 MET cc_start: 0.8940 (pmm) cc_final: 0.8375 (pmm) REVERT: D 243 LEU cc_start: 0.9537 (mm) cc_final: 0.9276 (mm) REVERT: D 268 LEU cc_start: 0.9449 (tt) cc_final: 0.8902 (tt) REVERT: D 286 LEU cc_start: 0.9379 (pp) cc_final: 0.9170 (pp) REVERT: D 302 PHE cc_start: 0.8461 (t80) cc_final: 0.8247 (t80) REVERT: D 319 GLU cc_start: 0.9659 (pp20) cc_final: 0.9415 (pp20) REVERT: D 327 GLN cc_start: 0.8461 (pt0) cc_final: 0.7935 (tm-30) REVERT: D 344 MET cc_start: 0.8710 (ppp) cc_final: 0.8377 (ppp) REVERT: D 388 MET cc_start: 0.8994 (mpp) cc_final: 0.8531 (mpp) REVERT: D 410 ASP cc_start: 0.9097 (p0) cc_final: 0.8874 (p0) REVERT: D 516 PHE cc_start: 0.8558 (m-80) cc_final: 0.8312 (m-10) REVERT: D 550 MET cc_start: 0.6848 (pmm) cc_final: 0.6479 (pmm) REVERT: D 562 ILE cc_start: 0.9477 (tp) cc_final: 0.8312 (pt) REVERT: D 574 LEU cc_start: 0.9606 (tp) cc_final: 0.9401 (tp) REVERT: D 575 PHE cc_start: 0.8630 (t80) cc_final: 0.8204 (t80) REVERT: D 639 LEU cc_start: 0.8009 (mp) cc_final: 0.7779 (mp) REVERT: E 158 MET cc_start: 0.8555 (tpp) cc_final: 0.8284 (tpp) REVERT: E 218 GLU cc_start: 0.9502 (tt0) cc_final: 0.8990 (tm-30) REVERT: E 275 MET cc_start: 0.9489 (mpp) cc_final: 0.9224 (mpp) REVERT: E 338 ARG cc_start: 0.8585 (mmt90) cc_final: 0.8100 (tpt90) REVERT: E 379 GLU cc_start: 0.9101 (tp30) cc_final: 0.8826 (tp30) REVERT: E 388 MET cc_start: 0.8911 (mmp) cc_final: 0.8503 (mmm) REVERT: E 452 PHE cc_start: 0.8587 (m-80) cc_final: 0.8205 (m-80) REVERT: E 470 GLU cc_start: 0.8707 (tt0) cc_final: 0.7809 (tm-30) REVERT: E 515 LEU cc_start: 0.9204 (mm) cc_final: 0.8982 (mm) REVERT: E 517 TYR cc_start: 0.7789 (p90) cc_final: 0.7079 (p90) REVERT: E 538 ASN cc_start: 0.9119 (t0) cc_final: 0.8587 (m110) REVERT: E 542 ILE cc_start: 0.9548 (tp) cc_final: 0.9329 (tp) REVERT: E 563 PHE cc_start: 0.9219 (m-10) cc_final: 0.8907 (m-80) REVERT: E 567 ARG cc_start: 0.8755 (ptp-170) cc_final: 0.8143 (ttp-110) REVERT: E 639 LEU cc_start: 0.9212 (pp) cc_final: 0.8980 (pp) REVERT: E 736 PHE cc_start: 0.8897 (m-80) cc_final: 0.8574 (m-10) REVERT: E 741 ARG cc_start: 0.9016 (tpm170) cc_final: 0.8574 (mmt-90) REVERT: A 64 ARG cc_start: 0.8720 (tpt90) cc_final: 0.8064 (mmm160) REVERT: A 84 MET cc_start: 0.9104 (mpp) cc_final: 0.8878 (mpp) REVERT: A 135 LEU cc_start: 0.9179 (tp) cc_final: 0.8975 (tp) REVERT: A 275 MET cc_start: 0.9515 (mtm) cc_final: 0.9215 (mtt) REVERT: A 344 MET cc_start: 0.8814 (mmm) cc_final: 0.7991 (mmm) REVERT: A 516 PHE cc_start: 0.8879 (m-80) cc_final: 0.8021 (m-80) REVERT: A 561 GLU cc_start: 0.9196 (tt0) cc_final: 0.8698 (tm-30) REVERT: A 651 LYS cc_start: 0.9391 (pttt) cc_final: 0.8990 (tmtt) REVERT: F 204 ASP cc_start: 0.8976 (m-30) cc_final: 0.8131 (p0) REVERT: F 253 LEU cc_start: 0.9705 (mm) cc_final: 0.9501 (mm) REVERT: F 269 ILE cc_start: 0.9644 (mt) cc_final: 0.9170 (mt) REVERT: F 270 ASN cc_start: 0.9396 (t0) cc_final: 0.8941 (t0) REVERT: F 348 ASN cc_start: 0.9100 (t0) cc_final: 0.8829 (p0) REVERT: F 440 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8108 (pp20) REVERT: F 495 TYR cc_start: 0.8626 (m-80) cc_final: 0.7897 (m-10) REVERT: F 565 LYS cc_start: 0.9313 (ptmm) cc_final: 0.8867 (pttp) REVERT: F 609 ASP cc_start: 0.8969 (m-30) cc_final: 0.8675 (m-30) REVERT: F 611 MET cc_start: 0.8314 (pmm) cc_final: 0.7936 (pmm) REVERT: F 678 MET cc_start: 0.8679 (mmt) cc_final: 0.8130 (mpp) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.4860 time to fit residues: 500.1844 Evaluate side-chains 504 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 192 optimal weight: 0.0170 chunk 36 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS E 443 ASN E 460 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32516 Z= 0.224 Angle : 0.767 9.986 43942 Z= 0.381 Chirality : 0.050 0.283 4978 Planarity : 0.005 0.077 5767 Dihedral : 7.798 179.004 4446 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 30.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 4015 helix: -1.29 (0.12), residues: 1646 sheet: -1.54 (0.23), residues: 495 loop : -1.33 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 476 HIS 0.006 0.001 HIS F 735 PHE 0.034 0.002 PHE E 302 TYR 0.028 0.002 TYR A 203 ARG 0.008 0.001 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8484 (mmp) cc_final: 0.8169 (mmm) REVERT: B 51 LEU cc_start: 0.7307 (mp) cc_final: 0.6844 (mt) REVERT: B 78 SER cc_start: 0.9669 (m) cc_final: 0.9331 (t) REVERT: B 84 MET cc_start: 0.9179 (mmp) cc_final: 0.8769 (mmm) REVERT: B 130 LEU cc_start: 0.8551 (tt) cc_final: 0.7917 (mp) REVERT: B 163 PHE cc_start: 0.9139 (m-10) cc_final: 0.8881 (m-10) REVERT: B 220 VAL cc_start: 0.9404 (m) cc_final: 0.8774 (m) REVERT: B 239 ARG cc_start: 0.7627 (mmt180) cc_final: 0.7236 (mmt180) REVERT: B 244 TYR cc_start: 0.8580 (p90) cc_final: 0.8234 (p90) REVERT: B 275 MET cc_start: 0.9550 (mpp) cc_final: 0.8837 (mpp) REVERT: B 302 PHE cc_start: 0.8491 (t80) cc_final: 0.8053 (t80) REVERT: B 305 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8341 (mm-30) REVERT: B 363 PHE cc_start: 0.8143 (m-10) cc_final: 0.7912 (m-80) REVERT: B 366 GLU cc_start: 0.8777 (pm20) cc_final: 0.8520 (pm20) REVERT: B 379 GLU cc_start: 0.9054 (tp30) cc_final: 0.8254 (tt0) REVERT: B 388 MET cc_start: 0.8210 (mmp) cc_final: 0.7250 (mmm) REVERT: B 427 MET cc_start: 0.8931 (tpt) cc_final: 0.8668 (tpt) REVERT: B 508 MET cc_start: 0.4539 (mtp) cc_final: 0.4055 (mtm) REVERT: B 515 LEU cc_start: 0.9290 (mm) cc_final: 0.9057 (mm) REVERT: B 517 TYR cc_start: 0.8428 (p90) cc_final: 0.7416 (p90) REVERT: B 524 LYS cc_start: 0.8977 (mttt) cc_final: 0.8042 (pttt) REVERT: B 538 ASN cc_start: 0.9182 (t0) cc_final: 0.8762 (t0) REVERT: B 565 LYS cc_start: 0.9699 (pptt) cc_final: 0.9460 (pptt) REVERT: B 674 PHE cc_start: 0.9194 (m-80) cc_final: 0.8850 (m-10) REVERT: B 678 MET cc_start: 0.7974 (mtt) cc_final: 0.7103 (ptt) REVERT: B 757 MET cc_start: 0.8581 (ttt) cc_final: 0.8339 (tmm) REVERT: C 59 LEU cc_start: 0.8391 (tt) cc_final: 0.8059 (tt) REVERT: C 84 MET cc_start: 0.9188 (mpp) cc_final: 0.8469 (mpp) REVERT: C 131 PHE cc_start: 0.7764 (m-80) cc_final: 0.7396 (m-80) REVERT: C 163 PHE cc_start: 0.8901 (m-80) cc_final: 0.8215 (m-80) REVERT: C 201 VAL cc_start: 0.9119 (m) cc_final: 0.8683 (p) REVERT: C 203 TYR cc_start: 0.8751 (m-80) cc_final: 0.7981 (m-80) REVERT: C 221 GLU cc_start: 0.8372 (pt0) cc_final: 0.8017 (pp20) REVERT: C 269 ILE cc_start: 0.9305 (mp) cc_final: 0.9022 (mp) REVERT: C 285 ASN cc_start: 0.9054 (t160) cc_final: 0.8204 (t0) REVERT: C 288 LYS cc_start: 0.9456 (tttt) cc_final: 0.9055 (pttp) REVERT: C 291 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8892 (mt-10) REVERT: C 388 MET cc_start: 0.8731 (pmm) cc_final: 0.8331 (pmm) REVERT: C 423 ILE cc_start: 0.9616 (mt) cc_final: 0.9396 (mm) REVERT: C 442 MET cc_start: 0.9165 (mmp) cc_final: 0.8848 (tpp) REVERT: C 449 MET cc_start: 0.8773 (mmp) cc_final: 0.8053 (mmm) REVERT: C 515 LEU cc_start: 0.8977 (mm) cc_final: 0.8769 (mm) REVERT: C 567 ARG cc_start: 0.9202 (mtt180) cc_final: 0.8820 (mmm-85) REVERT: C 609 ASP cc_start: 0.9362 (m-30) cc_final: 0.8887 (m-30) REVERT: C 639 LEU cc_start: 0.6553 (mm) cc_final: 0.6279 (mm) REVERT: D 114 ILE cc_start: 0.6889 (pt) cc_final: 0.6416 (mp) REVERT: D 135 LEU cc_start: 0.8587 (mt) cc_final: 0.8305 (mt) REVERT: D 139 PHE cc_start: 0.9089 (m-80) cc_final: 0.8768 (m-80) REVERT: D 158 MET cc_start: 0.8031 (ppp) cc_final: 0.6990 (ppp) REVERT: D 199 ASN cc_start: 0.8845 (p0) cc_final: 0.8461 (p0) REVERT: D 219 MET cc_start: 0.8792 (pmm) cc_final: 0.8360 (pmm) REVERT: D 268 LEU cc_start: 0.9399 (tt) cc_final: 0.8656 (tt) REVERT: D 319 GLU cc_start: 0.9574 (pp20) cc_final: 0.9175 (pp20) REVERT: D 383 ILE cc_start: 0.9287 (pt) cc_final: 0.8976 (pt) REVERT: D 386 LYS cc_start: 0.9218 (ptmt) cc_final: 0.8944 (ptmm) REVERT: D 388 MET cc_start: 0.9075 (mpp) cc_final: 0.8576 (mpp) REVERT: D 410 ASP cc_start: 0.9032 (p0) cc_final: 0.8790 (p0) REVERT: D 508 MET cc_start: 0.2679 (ptt) cc_final: 0.1659 (ptt) REVERT: D 516 PHE cc_start: 0.8512 (m-80) cc_final: 0.8259 (m-10) REVERT: D 550 MET cc_start: 0.6784 (pmm) cc_final: 0.6367 (pmm) REVERT: D 561 GLU cc_start: 0.9325 (pp20) cc_final: 0.9005 (pp20) REVERT: D 562 ILE cc_start: 0.8865 (tp) cc_final: 0.8323 (pt) REVERT: D 575 PHE cc_start: 0.8580 (t80) cc_final: 0.8153 (t80) REVERT: D 639 LEU cc_start: 0.7958 (mp) cc_final: 0.7684 (mp) REVERT: E 158 MET cc_start: 0.8590 (tpp) cc_final: 0.8236 (tpp) REVERT: E 218 GLU cc_start: 0.9457 (tt0) cc_final: 0.8940 (tm-30) REVERT: E 219 MET cc_start: 0.9277 (ppp) cc_final: 0.9017 (ppp) REVERT: E 275 MET cc_start: 0.9486 (mpp) cc_final: 0.9206 (mpp) REVERT: E 291 GLU cc_start: 0.9287 (pt0) cc_final: 0.8309 (tp30) REVERT: E 338 ARG cc_start: 0.8577 (mmt90) cc_final: 0.7984 (tpt90) REVERT: E 379 GLU cc_start: 0.9106 (tp30) cc_final: 0.8748 (tp30) REVERT: E 388 MET cc_start: 0.8879 (mmp) cc_final: 0.8492 (mmm) REVERT: E 452 PHE cc_start: 0.8329 (m-80) cc_final: 0.7936 (m-80) REVERT: E 515 LEU cc_start: 0.9190 (mm) cc_final: 0.8938 (mm) REVERT: E 517 TYR cc_start: 0.7720 (p90) cc_final: 0.6983 (p90) REVERT: E 538 ASN cc_start: 0.9070 (t0) cc_final: 0.8434 (m110) REVERT: E 542 ILE cc_start: 0.9554 (tp) cc_final: 0.9321 (tp) REVERT: E 563 PHE cc_start: 0.9190 (m-10) cc_final: 0.8844 (m-80) REVERT: E 567 ARG cc_start: 0.8730 (ptp-170) cc_final: 0.8160 (ttp80) REVERT: E 572 CYS cc_start: 0.7373 (p) cc_final: 0.6738 (p) REVERT: E 635 ARG cc_start: 0.8746 (ptt-90) cc_final: 0.7947 (ptm160) REVERT: E 639 LEU cc_start: 0.9118 (pp) cc_final: 0.8752 (pp) REVERT: E 736 PHE cc_start: 0.8982 (m-80) cc_final: 0.8588 (m-10) REVERT: E 740 MET cc_start: 0.7989 (mmp) cc_final: 0.6437 (mmp) REVERT: E 741 ARG cc_start: 0.8973 (tpm170) cc_final: 0.8555 (mmt-90) REVERT: A 64 ARG cc_start: 0.8763 (tpt90) cc_final: 0.8066 (mmm160) REVERT: A 84 MET cc_start: 0.9086 (mpp) cc_final: 0.8864 (mpp) REVERT: A 135 LEU cc_start: 0.9135 (tp) cc_final: 0.8918 (tp) REVERT: A 275 MET cc_start: 0.9480 (mtm) cc_final: 0.9247 (mtt) REVERT: A 344 MET cc_start: 0.8913 (mmm) cc_final: 0.8209 (mmm) REVERT: A 515 LEU cc_start: 0.9305 (tp) cc_final: 0.9098 (mm) REVERT: A 516 PHE cc_start: 0.8933 (m-80) cc_final: 0.7842 (m-80) REVERT: A 561 GLU cc_start: 0.9139 (tt0) cc_final: 0.8609 (tm-30) REVERT: A 620 ILE cc_start: 0.9587 (pt) cc_final: 0.9379 (pt) REVERT: A 651 LYS cc_start: 0.9450 (pttt) cc_final: 0.9045 (tmtt) REVERT: A 661 LEU cc_start: 0.7758 (pp) cc_final: 0.7251 (pp) REVERT: F 204 ASP cc_start: 0.8940 (m-30) cc_final: 0.8036 (p0) REVERT: F 253 LEU cc_start: 0.9680 (mm) cc_final: 0.9480 (mm) REVERT: F 288 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8899 (ptpp) REVERT: F 348 ASN cc_start: 0.9002 (t0) cc_final: 0.8457 (p0) REVERT: F 417 GLU cc_start: 0.9501 (mp0) cc_final: 0.9145 (mp0) REVERT: F 427 MET cc_start: 0.7552 (tpp) cc_final: 0.6422 (tpp) REVERT: F 442 MET cc_start: 0.8604 (mmp) cc_final: 0.7584 (ptt) REVERT: F 458 GLN cc_start: 0.9042 (mp10) cc_final: 0.8759 (mp10) REVERT: F 470 GLU cc_start: 0.8435 (pp20) cc_final: 0.7378 (pm20) REVERT: F 495 TYR cc_start: 0.8503 (m-80) cc_final: 0.7784 (m-10) REVERT: F 565 LYS cc_start: 0.9295 (ptmm) cc_final: 0.8840 (pttp) REVERT: F 606 THR cc_start: 0.8934 (p) cc_final: 0.8636 (p) REVERT: F 611 MET cc_start: 0.8195 (pmm) cc_final: 0.7818 (pmm) REVERT: F 678 MET cc_start: 0.8835 (mmt) cc_final: 0.7931 (mpp) outliers start: 0 outliers final: 0 residues processed: 698 average time/residue: 0.4609 time to fit residues: 499.2296 Evaluate side-chains 533 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 0.7980 chunk 372 optimal weight: 4.9990 chunk 339 optimal weight: 0.6980 chunk 361 optimal weight: 0.3980 chunk 217 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 342 optimal weight: 0.9990 chunk 360 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 568 GLN ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32516 Z= 0.195 Angle : 0.777 11.032 43942 Z= 0.381 Chirality : 0.050 0.295 4978 Planarity : 0.006 0.149 5767 Dihedral : 7.406 179.319 4446 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 4015 helix: -1.14 (0.12), residues: 1662 sheet: -1.32 (0.23), residues: 479 loop : -1.32 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 476 HIS 0.007 0.001 HIS C 317 PHE 0.031 0.002 PHE B 563 TYR 0.026 0.002 TYR A 203 ARG 0.016 0.001 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8503 (mmp) cc_final: 0.8158 (mmm) REVERT: B 84 MET cc_start: 0.9051 (mmp) cc_final: 0.8528 (mmm) REVERT: B 130 LEU cc_start: 0.8479 (tt) cc_final: 0.8157 (mp) REVERT: B 220 VAL cc_start: 0.9424 (m) cc_final: 0.8876 (m) REVERT: B 239 ARG cc_start: 0.7785 (mmt180) cc_final: 0.7415 (mmt180) REVERT: B 244 TYR cc_start: 0.8399 (p90) cc_final: 0.8057 (p90) REVERT: B 275 MET cc_start: 0.9508 (mpp) cc_final: 0.8722 (mpp) REVERT: B 302 PHE cc_start: 0.8673 (t80) cc_final: 0.8348 (t80) REVERT: B 305 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 359 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7669 (ttt90) REVERT: B 366 GLU cc_start: 0.8558 (pm20) cc_final: 0.8288 (pm20) REVERT: B 379 GLU cc_start: 0.9038 (tp30) cc_final: 0.8278 (tt0) REVERT: B 388 MET cc_start: 0.8213 (mmp) cc_final: 0.7102 (mmm) REVERT: B 427 MET cc_start: 0.8701 (tpt) cc_final: 0.8476 (tpt) REVERT: B 508 MET cc_start: 0.5349 (mtp) cc_final: 0.5069 (mtm) REVERT: B 517 TYR cc_start: 0.8294 (p90) cc_final: 0.7297 (p90) REVERT: B 524 LYS cc_start: 0.8933 (mttt) cc_final: 0.7930 (pttt) REVERT: B 538 ASN cc_start: 0.9190 (t0) cc_final: 0.8480 (m110) REVERT: B 565 LYS cc_start: 0.9641 (pptt) cc_final: 0.9420 (pptt) REVERT: B 604 ILE cc_start: 0.9637 (pt) cc_final: 0.9429 (pt) REVERT: B 674 PHE cc_start: 0.9159 (m-80) cc_final: 0.8850 (m-10) REVERT: B 678 MET cc_start: 0.7874 (mtt) cc_final: 0.7022 (ptt) REVERT: B 736 PHE cc_start: 0.8963 (m-10) cc_final: 0.8739 (m-10) REVERT: C 59 LEU cc_start: 0.8416 (tt) cc_final: 0.8085 (tt) REVERT: C 84 MET cc_start: 0.9275 (mpp) cc_final: 0.8589 (mpp) REVERT: C 131 PHE cc_start: 0.7525 (m-80) cc_final: 0.7284 (m-80) REVERT: C 163 PHE cc_start: 0.8877 (m-80) cc_final: 0.8200 (m-80) REVERT: C 203 TYR cc_start: 0.8498 (m-80) cc_final: 0.7578 (m-80) REVERT: C 221 GLU cc_start: 0.8346 (pt0) cc_final: 0.7939 (pp20) REVERT: C 261 GLU cc_start: 0.8070 (pt0) cc_final: 0.6629 (pt0) REVERT: C 285 ASN cc_start: 0.8953 (t160) cc_final: 0.8075 (t0) REVERT: C 288 LYS cc_start: 0.9430 (tttt) cc_final: 0.9016 (pttp) REVERT: C 291 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8854 (mt-10) REVERT: C 388 MET cc_start: 0.8288 (pmm) cc_final: 0.7835 (pmm) REVERT: C 423 ILE cc_start: 0.9575 (mt) cc_final: 0.9339 (mm) REVERT: C 442 MET cc_start: 0.9198 (mmp) cc_final: 0.8924 (tpp) REVERT: C 449 MET cc_start: 0.8678 (mmp) cc_final: 0.7991 (mmm) REVERT: C 515 LEU cc_start: 0.8865 (mm) cc_final: 0.8637 (mm) REVERT: C 567 ARG cc_start: 0.9151 (mtt180) cc_final: 0.8709 (mmm-85) REVERT: C 609 ASP cc_start: 0.9369 (m-30) cc_final: 0.8877 (m-30) REVERT: C 639 LEU cc_start: 0.7144 (mm) cc_final: 0.6736 (mm) REVERT: C 696 LYS cc_start: 0.9747 (tppt) cc_final: 0.9359 (mtmm) REVERT: D 28 VAL cc_start: 0.8057 (t) cc_final: 0.7855 (t) REVERT: D 114 ILE cc_start: 0.6729 (pt) cc_final: 0.6299 (mp) REVERT: D 135 LEU cc_start: 0.8563 (mt) cc_final: 0.8209 (mt) REVERT: D 139 PHE cc_start: 0.9012 (m-80) cc_final: 0.8681 (m-80) REVERT: D 158 MET cc_start: 0.7893 (ppp) cc_final: 0.6944 (ppp) REVERT: D 187 GLU cc_start: 0.8590 (mp0) cc_final: 0.8318 (mp0) REVERT: D 199 ASN cc_start: 0.8849 (p0) cc_final: 0.8357 (p0) REVERT: D 219 MET cc_start: 0.8352 (pmm) cc_final: 0.7770 (pmm) REVERT: D 268 LEU cc_start: 0.9260 (tt) cc_final: 0.8847 (tt) REVERT: D 273 GLU cc_start: 0.8725 (mp0) cc_final: 0.8481 (mp0) REVERT: D 302 PHE cc_start: 0.8700 (t80) cc_final: 0.8293 (t80) REVERT: D 319 GLU cc_start: 0.9538 (pp20) cc_final: 0.9113 (pp20) REVERT: D 388 MET cc_start: 0.9007 (mpp) cc_final: 0.8571 (mpp) REVERT: D 410 ASP cc_start: 0.9022 (p0) cc_final: 0.8765 (p0) REVERT: D 516 PHE cc_start: 0.8477 (m-80) cc_final: 0.8225 (m-10) REVERT: D 550 MET cc_start: 0.6769 (pmm) cc_final: 0.6395 (pmm) REVERT: D 561 GLU cc_start: 0.9312 (pp20) cc_final: 0.8846 (pp20) REVERT: D 562 ILE cc_start: 0.8788 (tp) cc_final: 0.8340 (pt) REVERT: D 574 LEU cc_start: 0.9545 (tp) cc_final: 0.9313 (tp) REVERT: D 575 PHE cc_start: 0.8563 (t80) cc_final: 0.8131 (t80) REVERT: D 599 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8202 (mtt180) REVERT: E 158 MET cc_start: 0.8527 (tpp) cc_final: 0.8216 (tpp) REVERT: E 216 ILE cc_start: 0.9388 (pt) cc_final: 0.9102 (pt) REVERT: E 218 GLU cc_start: 0.9394 (tt0) cc_final: 0.8854 (tm-30) REVERT: E 219 MET cc_start: 0.9239 (ppp) cc_final: 0.9033 (ppp) REVERT: E 221 GLU cc_start: 0.8800 (pp20) cc_final: 0.8482 (tp30) REVERT: E 275 MET cc_start: 0.9422 (mpp) cc_final: 0.9172 (mpp) REVERT: E 291 GLU cc_start: 0.9274 (pt0) cc_final: 0.8298 (tp30) REVERT: E 314 GLU cc_start: 0.8523 (tp30) cc_final: 0.8292 (tp30) REVERT: E 338 ARG cc_start: 0.8535 (mmt90) cc_final: 0.7924 (tpt90) REVERT: E 379 GLU cc_start: 0.9019 (tp30) cc_final: 0.8619 (tp30) REVERT: E 383 ILE cc_start: 0.9644 (mt) cc_final: 0.9430 (mt) REVERT: E 388 MET cc_start: 0.8920 (mmp) cc_final: 0.8618 (mmm) REVERT: E 452 PHE cc_start: 0.8315 (m-80) cc_final: 0.7963 (m-80) REVERT: E 515 LEU cc_start: 0.9127 (mm) cc_final: 0.8906 (mm) REVERT: E 517 TYR cc_start: 0.7671 (p90) cc_final: 0.6918 (p90) REVERT: E 538 ASN cc_start: 0.9069 (t0) cc_final: 0.8384 (m110) REVERT: E 542 ILE cc_start: 0.9535 (tp) cc_final: 0.9290 (tp) REVERT: E 563 PHE cc_start: 0.9237 (m-10) cc_final: 0.8972 (m-80) REVERT: E 564 ASP cc_start: 0.9170 (m-30) cc_final: 0.8968 (m-30) REVERT: E 567 ARG cc_start: 0.8681 (ptp-170) cc_final: 0.7984 (ptp-170) REVERT: E 572 CYS cc_start: 0.7204 (p) cc_final: 0.6590 (p) REVERT: E 635 ARG cc_start: 0.8697 (ptt-90) cc_final: 0.7918 (ptm160) REVERT: E 639 LEU cc_start: 0.9141 (pp) cc_final: 0.8757 (pp) REVERT: E 736 PHE cc_start: 0.8975 (m-80) cc_final: 0.8576 (m-10) REVERT: E 740 MET cc_start: 0.7899 (mmp) cc_final: 0.6346 (mmp) REVERT: E 741 ARG cc_start: 0.8944 (tpm170) cc_final: 0.8498 (mmt-90) REVERT: A 50 GLN cc_start: 0.9299 (pp30) cc_final: 0.9015 (pp30) REVERT: A 64 ARG cc_start: 0.8842 (tpt90) cc_final: 0.8104 (mmm160) REVERT: A 135 LEU cc_start: 0.9136 (tp) cc_final: 0.8922 (tp) REVERT: A 275 MET cc_start: 0.9426 (mtm) cc_final: 0.9219 (mtt) REVERT: A 344 MET cc_start: 0.8849 (mmm) cc_final: 0.8077 (mmm) REVERT: A 349 ARG cc_start: 0.9339 (mmm-85) cc_final: 0.8912 (tpp80) REVERT: A 508 MET cc_start: 0.3720 (ptp) cc_final: 0.2444 (pmm) REVERT: A 516 PHE cc_start: 0.8971 (m-80) cc_final: 0.8069 (m-80) REVERT: A 561 GLU cc_start: 0.9101 (tt0) cc_final: 0.8777 (tm-30) REVERT: A 651 LYS cc_start: 0.9442 (pttt) cc_final: 0.9018 (tmtt) REVERT: F 204 ASP cc_start: 0.8902 (m-30) cc_final: 0.8000 (p0) REVERT: F 222 LEU cc_start: 0.9351 (tp) cc_final: 0.8762 (tp) REVERT: F 328 LEU cc_start: 0.9658 (tt) cc_final: 0.9455 (tp) REVERT: F 348 ASN cc_start: 0.8884 (t0) cc_final: 0.8344 (p0) REVERT: F 417 GLU cc_start: 0.9464 (mp0) cc_final: 0.9044 (mp0) REVERT: F 427 MET cc_start: 0.7260 (tpp) cc_final: 0.6038 (tpp) REVERT: F 442 MET cc_start: 0.8452 (mmp) cc_final: 0.7483 (ptm) REVERT: F 470 GLU cc_start: 0.8477 (pp20) cc_final: 0.7443 (pm20) REVERT: F 489 LEU cc_start: 0.8813 (mp) cc_final: 0.8460 (tp) REVERT: F 606 THR cc_start: 0.8983 (p) cc_final: 0.8759 (p) REVERT: F 609 ASP cc_start: 0.9349 (m-30) cc_final: 0.9101 (m-30) REVERT: F 611 MET cc_start: 0.8430 (pmm) cc_final: 0.8113 (pmm) REVERT: F 678 MET cc_start: 0.8762 (mmt) cc_final: 0.7925 (mpp) outliers start: 0 outliers final: 0 residues processed: 711 average time/residue: 0.4690 time to fit residues: 522.8201 Evaluate side-chains 561 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 0.9980 chunk 382 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 369 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 327 GLN D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 499 HIS ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32516 Z= 0.215 Angle : 0.780 12.212 43942 Z= 0.385 Chirality : 0.050 0.301 4978 Planarity : 0.005 0.092 5767 Dihedral : 7.311 174.978 4446 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 4015 helix: -1.06 (0.12), residues: 1651 sheet: -1.41 (0.23), residues: 476 loop : -1.24 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 551 HIS 0.007 0.001 HIS F 735 PHE 0.038 0.002 PHE E 302 TYR 0.059 0.002 TYR E 203 ARG 0.021 0.001 ARG C 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 683 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8480 (mmp) cc_final: 0.8172 (mmm) REVERT: B 84 MET cc_start: 0.9037 (mmp) cc_final: 0.8541 (mmm) REVERT: B 130 LEU cc_start: 0.8364 (tt) cc_final: 0.8026 (mp) REVERT: B 217 LYS cc_start: 0.9433 (tmmt) cc_final: 0.9033 (tmtt) REVERT: B 218 GLU cc_start: 0.8963 (pm20) cc_final: 0.8497 (pm20) REVERT: B 220 VAL cc_start: 0.9362 (m) cc_final: 0.8812 (m) REVERT: B 239 ARG cc_start: 0.7855 (mmt180) cc_final: 0.7501 (mmt180) REVERT: B 244 TYR cc_start: 0.8447 (p90) cc_final: 0.8132 (p90) REVERT: B 275 MET cc_start: 0.9558 (mpp) cc_final: 0.8838 (mpp) REVERT: B 302 PHE cc_start: 0.8847 (t80) cc_final: 0.8214 (t80) REVERT: B 305 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 344 MET cc_start: 0.9060 (tpt) cc_final: 0.8344 (tpt) REVERT: B 363 PHE cc_start: 0.8088 (m-10) cc_final: 0.7594 (m-80) REVERT: B 365 ARG cc_start: 0.8058 (ptt-90) cc_final: 0.7431 (ptt-90) REVERT: B 366 GLU cc_start: 0.8768 (pm20) cc_final: 0.8450 (pm20) REVERT: B 379 GLU cc_start: 0.9070 (tp30) cc_final: 0.8515 (pt0) REVERT: B 388 MET cc_start: 0.8379 (mmp) cc_final: 0.7282 (mmm) REVERT: B 427 MET cc_start: 0.8701 (tpt) cc_final: 0.8473 (tpt) REVERT: B 508 MET cc_start: 0.5986 (mtp) cc_final: 0.5770 (mtm) REVERT: B 517 TYR cc_start: 0.8402 (p90) cc_final: 0.7422 (p90) REVERT: B 524 LYS cc_start: 0.9050 (mttt) cc_final: 0.8082 (pttt) REVERT: B 538 ASN cc_start: 0.9155 (t0) cc_final: 0.8947 (t0) REVERT: B 550 MET cc_start: 0.6373 (mmm) cc_final: 0.5961 (tpp) REVERT: B 674 PHE cc_start: 0.9201 (m-80) cc_final: 0.8880 (m-80) REVERT: B 678 MET cc_start: 0.7900 (mtt) cc_final: 0.7036 (ptt) REVERT: C 59 LEU cc_start: 0.8327 (tt) cc_final: 0.7944 (tt) REVERT: C 84 MET cc_start: 0.9161 (mpp) cc_final: 0.8384 (mpp) REVERT: C 131 PHE cc_start: 0.7710 (m-80) cc_final: 0.7368 (m-80) REVERT: C 163 PHE cc_start: 0.8846 (m-80) cc_final: 0.8194 (m-80) REVERT: C 198 LEU cc_start: 0.8729 (tp) cc_final: 0.8478 (tp) REVERT: C 203 TYR cc_start: 0.8531 (m-10) cc_final: 0.7541 (m-80) REVERT: C 221 GLU cc_start: 0.8401 (pt0) cc_final: 0.8009 (pp20) REVERT: C 261 GLU cc_start: 0.8088 (pt0) cc_final: 0.6193 (pt0) REVERT: C 291 GLU cc_start: 0.9362 (mt-10) cc_final: 0.8885 (mt-10) REVERT: C 423 ILE cc_start: 0.9648 (mt) cc_final: 0.9400 (mm) REVERT: C 442 MET cc_start: 0.9269 (mmp) cc_final: 0.8939 (tpp) REVERT: C 449 MET cc_start: 0.8714 (mmp) cc_final: 0.8131 (mmm) REVERT: C 515 LEU cc_start: 0.8897 (mm) cc_final: 0.8696 (mm) REVERT: C 609 ASP cc_start: 0.9378 (m-30) cc_final: 0.8887 (m-30) REVERT: C 639 LEU cc_start: 0.7226 (mm) cc_final: 0.6796 (mm) REVERT: C 696 LYS cc_start: 0.9757 (tppt) cc_final: 0.9425 (mtmm) REVERT: D 114 ILE cc_start: 0.6418 (pt) cc_final: 0.5974 (mp) REVERT: D 135 LEU cc_start: 0.8617 (mt) cc_final: 0.8350 (mt) REVERT: D 139 PHE cc_start: 0.9059 (m-80) cc_final: 0.8824 (m-80) REVERT: D 158 MET cc_start: 0.7953 (ppp) cc_final: 0.6877 (ppp) REVERT: D 199 ASN cc_start: 0.8874 (p0) cc_final: 0.8372 (p0) REVERT: D 219 MET cc_start: 0.8543 (pmm) cc_final: 0.8013 (pmm) REVERT: D 268 LEU cc_start: 0.9342 (tt) cc_final: 0.7921 (tt) REVERT: D 302 PHE cc_start: 0.8641 (t80) cc_final: 0.8262 (t80) REVERT: D 319 GLU cc_start: 0.9563 (pp20) cc_final: 0.9120 (pp20) REVERT: D 383 ILE cc_start: 0.9275 (pt) cc_final: 0.8974 (pt) REVERT: D 386 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8699 (ptmm) REVERT: D 388 MET cc_start: 0.8917 (mpp) cc_final: 0.8595 (mpp) REVERT: D 397 GLU cc_start: 0.8877 (mp0) cc_final: 0.8591 (mp0) REVERT: D 410 ASP cc_start: 0.9115 (p0) cc_final: 0.8811 (p0) REVERT: D 508 MET cc_start: 0.2524 (ptt) cc_final: 0.1594 (ptt) REVERT: D 516 PHE cc_start: 0.8511 (m-80) cc_final: 0.8270 (m-10) REVERT: D 550 MET cc_start: 0.6270 (pmm) cc_final: 0.6062 (pmm) REVERT: D 561 GLU cc_start: 0.9175 (pp20) cc_final: 0.8789 (pp20) REVERT: D 562 ILE cc_start: 0.8927 (tp) cc_final: 0.8379 (pt) REVERT: D 574 LEU cc_start: 0.9513 (tp) cc_final: 0.9299 (tp) REVERT: D 575 PHE cc_start: 0.8571 (t80) cc_final: 0.8063 (t80) REVERT: D 599 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8291 (mtt180) REVERT: D 639 LEU cc_start: 0.7776 (mp) cc_final: 0.7552 (mp) REVERT: E 158 MET cc_start: 0.8554 (tpp) cc_final: 0.8233 (tpp) REVERT: E 218 GLU cc_start: 0.9378 (tt0) cc_final: 0.8562 (tm-30) REVERT: E 219 MET cc_start: 0.9257 (ppp) cc_final: 0.9048 (ppp) REVERT: E 275 MET cc_start: 0.9434 (mpp) cc_final: 0.9188 (mpp) REVERT: E 291 GLU cc_start: 0.9259 (pt0) cc_final: 0.8355 (tp30) REVERT: E 314 GLU cc_start: 0.8558 (tp30) cc_final: 0.8314 (tp30) REVERT: E 338 ARG cc_start: 0.8554 (mmt90) cc_final: 0.7972 (tpt90) REVERT: E 379 GLU cc_start: 0.9144 (tp30) cc_final: 0.8705 (tp30) REVERT: E 388 MET cc_start: 0.8926 (mmp) cc_final: 0.8630 (mmm) REVERT: E 450 ASP cc_start: 0.8159 (p0) cc_final: 0.7925 (p0) REVERT: E 452 PHE cc_start: 0.8341 (m-80) cc_final: 0.7970 (m-80) REVERT: E 470 GLU cc_start: 0.8411 (tt0) cc_final: 0.7604 (tm-30) REVERT: E 515 LEU cc_start: 0.9126 (mm) cc_final: 0.8900 (mm) REVERT: E 517 TYR cc_start: 0.7671 (p90) cc_final: 0.6916 (p90) REVERT: E 538 ASN cc_start: 0.9021 (t0) cc_final: 0.8349 (m110) REVERT: E 542 ILE cc_start: 0.9540 (tp) cc_final: 0.9293 (tp) REVERT: E 563 PHE cc_start: 0.9240 (m-10) cc_final: 0.8973 (m-80) REVERT: E 567 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.7940 (ptp-170) REVERT: E 572 CYS cc_start: 0.7210 (p) cc_final: 0.6659 (p) REVERT: E 635 ARG cc_start: 0.8756 (ptt-90) cc_final: 0.7913 (ptm160) REVERT: E 678 MET cc_start: 0.4572 (ttm) cc_final: 0.4270 (ttm) REVERT: E 736 PHE cc_start: 0.8983 (m-80) cc_final: 0.8505 (m-10) REVERT: E 741 ARG cc_start: 0.8944 (tpm170) cc_final: 0.8375 (ttp80) REVERT: A 43 GLN cc_start: 0.9615 (mp-120) cc_final: 0.9408 (mm-40) REVERT: A 50 GLN cc_start: 0.9307 (pp30) cc_final: 0.8962 (pp30) REVERT: A 64 ARG cc_start: 0.8864 (tpt90) cc_final: 0.8110 (mmm160) REVERT: A 135 LEU cc_start: 0.9137 (tp) cc_final: 0.8933 (tp) REVERT: A 275 MET cc_start: 0.9407 (mtm) cc_final: 0.9186 (mtt) REVERT: A 344 MET cc_start: 0.8756 (mmm) cc_final: 0.8016 (mmm) REVERT: A 516 PHE cc_start: 0.9020 (m-80) cc_final: 0.8100 (m-80) REVERT: A 561 GLU cc_start: 0.9241 (tt0) cc_final: 0.8591 (tm-30) REVERT: A 651 LYS cc_start: 0.9448 (pttt) cc_final: 0.9027 (tmtt) REVERT: F 204 ASP cc_start: 0.8954 (m-30) cc_final: 0.8038 (p0) REVERT: F 222 LEU cc_start: 0.9384 (tp) cc_final: 0.8761 (tp) REVERT: F 288 LYS cc_start: 0.9100 (ptpp) cc_final: 0.8816 (ptpp) REVERT: F 369 ILE cc_start: 0.9496 (mp) cc_final: 0.9253 (tt) REVERT: F 417 GLU cc_start: 0.9460 (mp0) cc_final: 0.9095 (mp0) REVERT: F 442 MET cc_start: 0.8594 (mmp) cc_final: 0.7732 (ptt) REVERT: F 458 GLN cc_start: 0.9007 (mp10) cc_final: 0.8736 (mp10) REVERT: F 470 GLU cc_start: 0.8522 (pp20) cc_final: 0.7485 (pm20) REVERT: F 489 LEU cc_start: 0.8866 (mp) cc_final: 0.8549 (tp) REVERT: F 606 THR cc_start: 0.8981 (p) cc_final: 0.8739 (p) REVERT: F 609 ASP cc_start: 0.9274 (m-30) cc_final: 0.8946 (m-30) REVERT: F 611 MET cc_start: 0.8231 (pmm) cc_final: 0.7985 (pmm) REVERT: F 678 MET cc_start: 0.8786 (mmt) cc_final: 0.7960 (mpp) outliers start: 0 outliers final: 0 residues processed: 683 average time/residue: 0.4782 time to fit residues: 511.0135 Evaluate side-chains 530 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 253 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 320 optimal weight: 5.9990 chunk 134 optimal weight: 0.0670 chunk 328 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 183 HIS D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.092635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069288 restraints weight = 135857.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071829 restraints weight = 93723.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073647 restraints weight = 70453.111| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32516 Z= 0.197 Angle : 0.773 12.694 43942 Z= 0.378 Chirality : 0.050 0.307 4978 Planarity : 0.005 0.065 5767 Dihedral : 7.181 171.325 4446 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4015 helix: -1.03 (0.12), residues: 1662 sheet: -1.32 (0.23), residues: 481 loop : -1.26 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 551 HIS 0.007 0.001 HIS B 317 PHE 0.019 0.001 PHE B 563 TYR 0.042 0.002 TYR E 203 ARG 0.011 0.001 ARG E 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8798.86 seconds wall clock time: 158 minutes 33.69 seconds (9513.69 seconds total)