Starting phenix.real_space_refine on Tue Apr 9 22:08:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzb_24088/04_2024/7mzb_24088_updated.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11557 2.51 5 N 2814 2.21 5 O 3134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 701": "NH1" <-> "NH2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17607 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4363 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 522} Chain: "D" Number of atoms: 4351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4351 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4357 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4357 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.28, per 1000 atoms: 0.53 Number of scatterers: 17607 At special positions: 0 Unit cell: (125.1, 125.1, 112.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 1 15.00 Na 1 11.00 O 3134 8.00 N 2814 7.00 C 11557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 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: 7.12 Conformation dependent library (CDL) restraints added in 3.2 seconds 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 58.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.367A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.245A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.673A pdb=" N SER A 540 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.998A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.978A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 673 through 686 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.626A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.357A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 5.016A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 505 through 508 No H-bonds generated for 'chain 'D' and resid 505 through 508' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.736A pdb=" N SER D 540 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 598 removed outlier: 4.169A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.977A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 711 removed outlier: 3.858A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 719 No H-bonds generated for 'chain 'D' and resid 717 through 719' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.519A pdb=" N PHE B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 4.349A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 453 removed outlier: 4.983A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.523A pdb=" N SER B 540 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.746A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 598 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.909A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.555A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.422A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 416 through 453 removed outlier: 5.019A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 558 removed outlier: 3.987A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 4.159A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.935A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 673 through 688 Processing helix chain 'C' and resid 690 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.957A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.894A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.853A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.972A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2451 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: 4.81 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2720 1.30 - 1.43: 5135 1.43 - 1.56: 10015 1.56 - 1.69: 14 1.69 - 1.82: 164 Bond restraints: 18048 Sorted by residual: bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.187 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.194 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.195 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAV 6EU C 901 " pdb=" CBB 6EU C 901 " ideal model delta sigma weight residual 1.330 1.522 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" CAV 6EU B 901 " pdb=" CBB 6EU B 901 " ideal model delta sigma weight residual 1.330 1.521 -0.191 2.00e-02 2.50e+03 9.11e+01 ... (remaining 18043 not shown) Histogram of bond angle deviations from ideal: 96.19 - 103.76: 199 103.76 - 111.33: 7802 111.33 - 118.90: 6533 118.90 - 126.47: 9726 126.47 - 134.05: 218 Bond angle restraints: 24478 Sorted by residual: angle pdb=" CG ARG D 557 " pdb=" CD ARG D 557 " pdb=" NE ARG D 557 " ideal model delta sigma weight residual 112.00 125.26 -13.26 2.20e+00 2.07e-01 3.63e+01 angle pdb=" CD ARG D 557 " pdb=" NE ARG D 557 " pdb=" CZ ARG D 557 " ideal model delta sigma weight residual 124.40 132.26 -7.86 1.40e+00 5.10e-01 3.15e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 129.90 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" N SER D 722 " pdb=" CA SER D 722 " pdb=" CB SER D 722 " ideal model delta sigma weight residual 114.17 108.66 5.51 1.14e+00 7.69e-01 2.34e+01 angle pdb=" CBM 6EU B 901 " pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 110.82 125.03 -14.21 3.00e+00 1.11e-01 2.24e+01 ... (remaining 24473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 10462 23.44 - 46.87: 271 46.87 - 70.31: 54 70.31 - 93.75: 16 93.75 - 117.18: 1 Dihedral angle restraints: 10804 sinusoidal: 4481 harmonic: 6323 Sorted by residual: dihedral pdb=" CA TYR C 653 " pdb=" C TYR C 653 " pdb=" N ASP C 654 " pdb=" CA ASP C 654 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE C 429 " pdb=" C PHE C 429 " pdb=" N VAL C 430 " pdb=" CA VAL C 430 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CG ARG D 557 " pdb=" CD ARG D 557 " pdb=" NE ARG D 557 " pdb=" CZ ARG D 557 " ideal model delta sinusoidal sigma weight residual -90.00 -3.94 -86.06 2 1.50e+01 4.44e-03 2.12e+01 ... (remaining 10801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 2746 0.997 - 1.995: 0 1.995 - 2.992: 0 2.992 - 3.990: 0 3.990 - 4.987: 2 Chirality restraints: 2748 Sorted by residual: chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.49 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" C XJ7 A 801 " pdb=" O XJ7 A 801 " pdb=" C1 XJ7 A 801 " pdb=" C25 XJ7 A 801 " both_signs ideal model delta sigma weight residual False 2.51 -2.45 4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" CAO 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAR 6EU D 901 " pdb=" CAW 6EU D 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.76 0.52 2.00e-01 2.50e+01 6.85e+00 ... (remaining 2745 not shown) Planarity restraints: 3013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " 0.101 2.00e-02 2.50e+03 1.79e-01 3.19e+02 pdb=" CAV 6EU D 901 " -0.309 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " 0.105 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " 0.093 2.00e-02 2.50e+03 1.66e-01 2.74e+02 pdb=" CAV 6EU C 901 " -0.287 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " 0.098 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " -0.081 2.00e-02 2.50e+03 1.44e-01 2.06e+02 pdb=" CAV 6EU B 901 " 0.249 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " -0.083 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " -0.085 2.00e-02 2.50e+03 ... (remaining 3010 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 204 2.60 - 3.18: 16704 3.18 - 3.75: 27812 3.75 - 4.33: 38741 4.33 - 4.90: 63081 Nonbonded interactions: 146542 Sorted by model distance: nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.029 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.087 2.440 nonbonded pdb=" O ILE C 387 " pdb=" OG SER C 394 " model vdw 2.105 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.125 2.440 nonbonded pdb=" O ILE B 689 " pdb=" OG SER B 693 " model vdw 2.148 2.440 ... (remaining 146537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 194 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 752)) selection = (chain 'B' and (resid 194 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 752)) selection = (chain 'C' and (resid 194 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 752)) selection = (chain 'D' and resid 194 through 752) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.990 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.190 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.235 18048 Z= 0.708 Angle : 0.919 14.523 24478 Z= 0.479 Chirality : 0.144 4.987 2748 Planarity : 0.007 0.179 3013 Dihedral : 12.200 117.183 6743 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2137 helix: 1.36 (0.14), residues: 1357 sheet: -1.25 (0.56), residues: 71 loop : -1.42 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 740 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.002 PHE A 304 TYR 0.026 0.002 TYR B 511 ARG 0.008 0.001 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1054 time to evaluate : 1.991 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: A 222 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 226 ASP cc_start: 0.8012 (t0) cc_final: 0.7742 (t0) REVERT: A 237 LYS cc_start: 0.8462 (mttt) cc_final: 0.8199 (mttp) REVERT: A 250 LEU cc_start: 0.8687 (mt) cc_final: 0.8483 (mp) REVERT: A 311 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9150 (mm-30) REVERT: A 351 TYR cc_start: 0.8588 (t80) cc_final: 0.8296 (t80) REVERT: A 372 TRP cc_start: 0.8349 (p-90) cc_final: 0.7400 (p-90) REVERT: A 378 HIS cc_start: 0.8646 (p-80) cc_final: 0.8150 (p-80) REVERT: A 411 ASP cc_start: 0.8993 (m-30) cc_final: 0.8793 (t0) REVERT: A 431 LYS cc_start: 0.8906 (tttt) cc_final: 0.8608 (ttpt) REVERT: A 432 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8345 (mtm110) REVERT: A 519 GLN cc_start: 0.9076 (tt0) cc_final: 0.8754 (tt0) REVERT: A 536 GLU cc_start: 0.8768 (mp0) cc_final: 0.8276 (mp0) REVERT: A 551 ASN cc_start: 0.9206 (m-40) cc_final: 0.8878 (m-40) REVERT: A 675 LEU cc_start: 0.9175 (mt) cc_final: 0.8939 (mm) REVERT: A 688 LYS cc_start: 0.9356 (mttt) cc_final: 0.8836 (mmtm) REVERT: A 693 SER cc_start: 0.9743 (m) cc_final: 0.9517 (p) REVERT: A 703 ILE cc_start: 0.9519 (tp) cc_final: 0.9171 (tp) REVERT: A 707 ASP cc_start: 0.8637 (m-30) cc_final: 0.8224 (m-30) REVERT: D 198 TYR cc_start: 0.6773 (t80) cc_final: 0.6539 (t80) REVERT: D 265 LYS cc_start: 0.9614 (mttt) cc_final: 0.9403 (mttp) REVERT: D 288 LEU cc_start: 0.9413 (mt) cc_final: 0.9207 (mt) REVERT: D 310 ASN cc_start: 0.9340 (t0) cc_final: 0.8968 (t0) REVERT: D 311 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8928 (mm-30) REVERT: D 326 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8374 (mt-10) REVERT: D 372 TRP cc_start: 0.8473 (p-90) cc_final: 0.7536 (p-90) REVERT: D 412 MET cc_start: 0.9298 (mtm) cc_final: 0.9077 (mtp) REVERT: D 416 GLU cc_start: 0.7788 (tp30) cc_final: 0.7555 (tp30) REVERT: D 423 GLN cc_start: 0.8920 (tp40) cc_final: 0.8353 (tp-100) REVERT: D 427 ASP cc_start: 0.8979 (m-30) cc_final: 0.8514 (m-30) REVERT: D 438 PHE cc_start: 0.9238 (t80) cc_final: 0.8776 (t80) REVERT: D 442 CYS cc_start: 0.9278 (m) cc_final: 0.8836 (m) REVERT: D 471 ASP cc_start: 0.8161 (m-30) cc_final: 0.7839 (m-30) REVERT: D 536 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: D 569 ILE cc_start: 0.9415 (mm) cc_final: 0.8792 (mm) REVERT: D 572 MET cc_start: 0.8561 (mmt) cc_final: 0.8348 (mmt) REVERT: D 576 ASP cc_start: 0.8782 (m-30) cc_final: 0.8563 (m-30) REVERT: D 579 ARG cc_start: 0.8842 (mtm180) cc_final: 0.8475 (mtt-85) REVERT: D 582 PHE cc_start: 0.8863 (t80) cc_final: 0.8619 (m-80) REVERT: D 592 SER cc_start: 0.9396 (m) cc_final: 0.9165 (p) REVERT: D 660 ILE cc_start: 0.9754 (tp) cc_final: 0.9403 (tp) REVERT: D 678 LEU cc_start: 0.9441 (tp) cc_final: 0.9220 (tp) REVERT: D 689 ILE cc_start: 0.9274 (pt) cc_final: 0.9061 (pt) REVERT: D 718 LYS cc_start: 0.8702 (ptmt) cc_final: 0.8395 (ptmm) REVERT: B 207 ILE cc_start: 0.9215 (mt) cc_final: 0.8972 (mt) REVERT: B 213 ASN cc_start: 0.9015 (t0) cc_final: 0.8606 (t0) REVERT: B 216 LEU cc_start: 0.9455 (mt) cc_final: 0.9065 (mt) REVERT: B 328 ILE cc_start: 0.9329 (mt) cc_final: 0.9099 (tt) REVERT: B 360 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8817 (Cg_endo) REVERT: B 378 HIS cc_start: 0.9163 (p-80) cc_final: 0.8796 (p-80) REVERT: B 389 THR cc_start: 0.9126 (t) cc_final: 0.8868 (t) REVERT: B 423 GLN cc_start: 0.8951 (tp40) cc_final: 0.8547 (tp-100) REVERT: B 478 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 536 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 551 ASN cc_start: 0.9626 (m-40) cc_final: 0.9411 (m-40) REVERT: B 560 GLN cc_start: 0.9001 (tp40) cc_final: 0.6669 (tp-100) REVERT: B 578 CYS cc_start: 0.8941 (m) cc_final: 0.8562 (m) REVERT: B 582 PHE cc_start: 0.9172 (t80) cc_final: 0.8899 (t80) REVERT: B 656 LYS cc_start: 0.8816 (tttt) cc_final: 0.8514 (ttpt) REVERT: B 660 ILE cc_start: 0.9550 (tp) cc_final: 0.9333 (tp) REVERT: B 688 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8570 (mptt) REVERT: B 697 TRP cc_start: 0.8729 (t60) cc_final: 0.8435 (t60) REVERT: B 745 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8774 (m-30) REVERT: C 198 TYR cc_start: 0.8276 (m-80) cc_final: 0.7813 (m-10) REVERT: C 202 GLN cc_start: 0.8346 (tt0) cc_final: 0.8046 (tm-30) REVERT: C 213 ASN cc_start: 0.8971 (t0) cc_final: 0.8702 (t0) REVERT: C 219 LEU cc_start: 0.9432 (mt) cc_final: 0.9018 (mt) REVERT: C 226 ASP cc_start: 0.7653 (t0) cc_final: 0.7438 (t70) REVERT: C 273 GLN cc_start: 0.7990 (tp40) cc_final: 0.7290 (tt0) REVERT: C 274 PRO cc_start: 0.8440 (Cg_endo) cc_final: 0.8209 (Cg_exo) REVERT: C 313 LEU cc_start: 0.9493 (mt) cc_final: 0.9287 (mt) REVERT: C 319 LEU cc_start: 0.9229 (mt) cc_final: 0.8939 (mt) REVERT: C 368 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8375 (ttpp) REVERT: C 372 TRP cc_start: 0.8481 (p-90) cc_final: 0.7098 (p-90) REVERT: C 378 HIS cc_start: 0.8808 (p-80) cc_final: 0.8468 (p90) REVERT: C 385 SER cc_start: 0.9531 (t) cc_final: 0.9264 (p) REVERT: C 392 LYS cc_start: 0.8785 (mttt) cc_final: 0.8275 (mtpp) REVERT: C 406 THR cc_start: 0.7756 (m) cc_final: 0.7537 (p) REVERT: C 412 MET cc_start: 0.9152 (mtp) cc_final: 0.8936 (mtp) REVERT: C 431 LYS cc_start: 0.9371 (tttt) cc_final: 0.8934 (ttpp) REVERT: C 465 LEU cc_start: 0.9083 (tp) cc_final: 0.8785 (tp) REVERT: C 471 ASP cc_start: 0.8338 (m-30) cc_final: 0.7984 (t70) REVERT: C 510 SER cc_start: 0.8757 (m) cc_final: 0.6837 (p) REVERT: C 556 THR cc_start: 0.9529 (p) cc_final: 0.9324 (p) REVERT: C 578 CYS cc_start: 0.9111 (m) cc_final: 0.8466 (m) REVERT: C 656 LYS cc_start: 0.8543 (pttt) cc_final: 0.8216 (ttpp) REVERT: C 660 ILE cc_start: 0.9546 (tp) cc_final: 0.9340 (tp) REVERT: C 684 GLU cc_start: 0.8569 (tp30) cc_final: 0.7465 (tp30) REVERT: C 687 ASN cc_start: 0.9142 (t0) cc_final: 0.8722 (t0) REVERT: C 746 GLU cc_start: 0.8622 (tp30) cc_final: 0.8395 (tm-30) outliers start: 16 outliers final: 2 residues processed: 1059 average time/residue: 0.3143 time to fit residues: 485.3492 Evaluate side-chains 731 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 726 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 745 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN D 419 ASN D 494 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN B 560 GLN C 206 HIS ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18048 Z= 0.206 Angle : 0.648 11.302 24478 Z= 0.333 Chirality : 0.041 0.334 2748 Planarity : 0.004 0.047 3013 Dihedral : 8.059 100.997 2683 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 3.32 % Allowed : 15.03 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2137 helix: 1.60 (0.14), residues: 1329 sheet: -0.59 (0.63), residues: 56 loop : -1.30 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 740 HIS 0.012 0.002 HIS B 358 PHE 0.024 0.002 PHE C 720 TYR 0.020 0.001 TYR D 555 ARG 0.012 0.001 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 861 time to evaluate : 2.014 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: A 197 SER cc_start: 0.8161 (p) cc_final: 0.7924 (m) REVERT: A 226 ASP cc_start: 0.7988 (t0) cc_final: 0.7713 (t0) REVERT: A 319 LEU cc_start: 0.9460 (mt) cc_final: 0.9199 (mp) REVERT: A 372 TRP cc_start: 0.8359 (p-90) cc_final: 0.7289 (p-90) REVERT: A 378 HIS cc_start: 0.8468 (p-80) cc_final: 0.8071 (p-80) REVERT: A 411 ASP cc_start: 0.8993 (m-30) cc_final: 0.8757 (t0) REVERT: A 432 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8258 (mtm110) REVERT: A 519 GLN cc_start: 0.9022 (tt0) cc_final: 0.8812 (tt0) REVERT: A 534 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6899 (mmm-85) REVERT: A 551 ASN cc_start: 0.9243 (m-40) cc_final: 0.8856 (m110) REVERT: A 597 THR cc_start: 0.9628 (m) cc_final: 0.9364 (p) REVERT: A 703 ILE cc_start: 0.9460 (tp) cc_final: 0.9038 (tp) REVERT: A 707 ASP cc_start: 0.8453 (m-30) cc_final: 0.7967 (m-30) REVERT: D 266 PHE cc_start: 0.9089 (t80) cc_final: 0.8845 (t80) REVERT: D 288 LEU cc_start: 0.9407 (mt) cc_final: 0.9162 (mt) REVERT: D 310 ASN cc_start: 0.9215 (t0) cc_final: 0.8914 (t0) REVERT: D 311 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8980 (mm-30) REVERT: D 423 GLN cc_start: 0.8933 (tp40) cc_final: 0.8289 (tp-100) REVERT: D 427 ASP cc_start: 0.8884 (m-30) cc_final: 0.8492 (m-30) REVERT: D 438 PHE cc_start: 0.9201 (t80) cc_final: 0.8726 (t80) REVERT: D 471 ASP cc_start: 0.8080 (m-30) cc_final: 0.7738 (m-30) REVERT: D 479 ILE cc_start: 0.9156 (mt) cc_final: 0.8937 (tp) REVERT: D 494 GLN cc_start: 0.8719 (mt0) cc_final: 0.8501 (mt0) REVERT: D 551 ASN cc_start: 0.9614 (m-40) cc_final: 0.9361 (m-40) REVERT: D 579 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8565 (mtt-85) REVERT: D 582 PHE cc_start: 0.8910 (t80) cc_final: 0.8583 (m-80) REVERT: D 660 ILE cc_start: 0.9711 (tp) cc_final: 0.9423 (tp) REVERT: D 664 LEU cc_start: 0.9496 (mt) cc_final: 0.9269 (mp) REVERT: D 725 LEU cc_start: 0.9269 (mt) cc_final: 0.8869 (mp) REVERT: B 213 ASN cc_start: 0.8905 (t0) cc_final: 0.8668 (t0) REVERT: B 216 LEU cc_start: 0.9308 (mt) cc_final: 0.9074 (mt) REVERT: B 254 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9411 (tp) REVERT: B 309 TYR cc_start: 0.9093 (t80) cc_final: 0.8717 (t80) REVERT: B 326 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 360 PRO cc_start: 0.8826 (Cg_exo) cc_final: 0.7421 (Cg_endo) REVERT: B 385 SER cc_start: 0.9255 (t) cc_final: 0.9035 (m) REVERT: B 423 GLN cc_start: 0.8936 (tp40) cc_final: 0.8688 (tp-100) REVERT: B 428 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7793 (ptm160) REVERT: B 431 LYS cc_start: 0.9232 (tttt) cc_final: 0.8920 (ttpt) REVERT: B 551 ASN cc_start: 0.9614 (m-40) cc_final: 0.9410 (m-40) REVERT: B 578 CYS cc_start: 0.8884 (m) cc_final: 0.8441 (m) REVERT: B 628 ASN cc_start: 0.7700 (t0) cc_final: 0.7154 (t0) REVERT: B 656 LYS cc_start: 0.8862 (tttt) cc_final: 0.8551 (ttpt) REVERT: B 660 ILE cc_start: 0.9532 (tp) cc_final: 0.9299 (tp) REVERT: B 678 LEU cc_start: 0.9339 (tp) cc_final: 0.9117 (tp) REVERT: C 202 GLN cc_start: 0.8258 (tt0) cc_final: 0.8028 (tp40) REVERT: C 226 ASP cc_start: 0.7681 (t0) cc_final: 0.7461 (t70) REVERT: C 234 ASP cc_start: 0.8838 (m-30) cc_final: 0.8613 (m-30) REVERT: C 273 GLN cc_start: 0.8052 (tp40) cc_final: 0.7301 (tt0) REVERT: C 274 PRO cc_start: 0.8437 (Cg_endo) cc_final: 0.8229 (Cg_exo) REVERT: C 276 ASP cc_start: 0.8654 (t0) cc_final: 0.8357 (t0) REVERT: C 372 TRP cc_start: 0.8435 (p-90) cc_final: 0.7145 (p-90) REVERT: C 383 ASP cc_start: 0.7843 (t70) cc_final: 0.7551 (t70) REVERT: C 385 SER cc_start: 0.9495 (t) cc_final: 0.9212 (p) REVERT: C 392 LYS cc_start: 0.8566 (mttt) cc_final: 0.8327 (mtpp) REVERT: C 406 THR cc_start: 0.7647 (m) cc_final: 0.7445 (p) REVERT: C 410 HIS cc_start: 0.7466 (m170) cc_final: 0.7032 (m170) REVERT: C 465 LEU cc_start: 0.9070 (tp) cc_final: 0.8850 (tp) REVERT: C 510 SER cc_start: 0.8438 (m) cc_final: 0.7644 (p) REVERT: C 513 GLU cc_start: 0.8647 (mp0) cc_final: 0.8360 (mp0) REVERT: C 570 GLU cc_start: 0.8860 (tt0) cc_final: 0.8659 (tt0) REVERT: C 578 CYS cc_start: 0.9021 (m) cc_final: 0.8421 (m) REVERT: C 631 TYR cc_start: 0.8591 (t80) cc_final: 0.8291 (t80) REVERT: C 654 ASP cc_start: 0.8270 (t0) cc_final: 0.7783 (t0) REVERT: C 656 LYS cc_start: 0.8550 (pttt) cc_final: 0.8246 (ttpp) REVERT: C 660 ILE cc_start: 0.9543 (tp) cc_final: 0.9311 (tp) REVERT: C 717 ARG cc_start: 0.6312 (mmp80) cc_final: 0.5967 (mmm160) outliers start: 63 outliers final: 37 residues processed: 873 average time/residue: 0.2723 time to fit residues: 362.6147 Evaluate side-chains 771 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 733 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 358 HIS A 652 ASN D 260 GLN D 320 HIS D 419 ASN C 206 HIS C 228 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN C 652 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18048 Z= 0.261 Angle : 0.637 9.176 24478 Z= 0.329 Chirality : 0.041 0.267 2748 Planarity : 0.004 0.047 3013 Dihedral : 7.286 89.210 2670 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.27 % Favored : 93.54 % Rotamer: Outliers : 4.32 % Allowed : 17.77 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2137 helix: 1.58 (0.14), residues: 1323 sheet: -0.42 (0.64), residues: 61 loop : -1.32 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 372 HIS 0.019 0.001 HIS A 358 PHE 0.024 0.002 PHE C 439 TYR 0.019 0.001 TYR A 435 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 754 time to evaluate : 1.923 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: A 197 SER cc_start: 0.8132 (p) cc_final: 0.7898 (m) REVERT: A 226 ASP cc_start: 0.7944 (t0) cc_final: 0.7685 (t0) REVERT: A 310 ASN cc_start: 0.9467 (t0) cc_final: 0.9264 (t0) REVERT: A 323 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7583 (tt) REVERT: A 372 TRP cc_start: 0.8385 (p-90) cc_final: 0.7348 (p-90) REVERT: A 378 HIS cc_start: 0.8404 (p-80) cc_final: 0.8091 (p-80) REVERT: A 411 ASP cc_start: 0.8947 (m-30) cc_final: 0.8728 (t0) REVERT: A 432 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8244 (mtm110) REVERT: A 551 ASN cc_start: 0.9269 (m-40) cc_final: 0.8883 (m110) REVERT: A 597 THR cc_start: 0.9642 (m) cc_final: 0.9390 (p) REVERT: A 675 LEU cc_start: 0.9029 (mt) cc_final: 0.8780 (mt) REVERT: A 703 ILE cc_start: 0.9496 (tp) cc_final: 0.9136 (tp) REVERT: A 707 ASP cc_start: 0.8485 (m-30) cc_final: 0.8026 (m-30) REVERT: D 266 PHE cc_start: 0.9104 (t80) cc_final: 0.8862 (t80) REVERT: D 288 LEU cc_start: 0.9471 (mt) cc_final: 0.9231 (mt) REVERT: D 304 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8314 (p90) REVERT: D 310 ASN cc_start: 0.9262 (t0) cc_final: 0.8934 (t0) REVERT: D 311 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8992 (mm-30) REVERT: D 326 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8177 (mt-10) REVERT: D 371 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6848 (mm-30) REVERT: D 372 TRP cc_start: 0.8059 (p-90) cc_final: 0.7687 (p-90) REVERT: D 419 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.9005 (m-40) REVERT: D 423 GLN cc_start: 0.9017 (tp40) cc_final: 0.8389 (tp-100) REVERT: D 427 ASP cc_start: 0.8901 (m-30) cc_final: 0.8562 (m-30) REVERT: D 471 ASP cc_start: 0.8095 (m-30) cc_final: 0.7794 (m-30) REVERT: D 479 ILE cc_start: 0.9207 (mt) cc_final: 0.9006 (tp) REVERT: D 499 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: D 551 ASN cc_start: 0.9594 (m-40) cc_final: 0.9340 (m-40) REVERT: D 582 PHE cc_start: 0.8959 (t80) cc_final: 0.8618 (m-10) REVERT: D 660 ILE cc_start: 0.9737 (tp) cc_final: 0.9427 (tp) REVERT: D 684 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8674 (tm-30) REVERT: D 697 TRP cc_start: 0.8804 (t60) cc_final: 0.8366 (t60) REVERT: D 718 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8167 (ptmm) REVERT: B 213 ASN cc_start: 0.8859 (t0) cc_final: 0.8581 (t0) REVERT: B 216 LEU cc_start: 0.9286 (mt) cc_final: 0.9047 (mt) REVERT: B 301 ASN cc_start: 0.8192 (t0) cc_final: 0.7935 (t0) REVERT: B 304 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8366 (p90) REVERT: B 309 TYR cc_start: 0.9140 (t80) cc_final: 0.8709 (t80) REVERT: B 404 SER cc_start: 0.5566 (m) cc_final: 0.5196 (t) REVERT: B 423 GLN cc_start: 0.8958 (tp40) cc_final: 0.8657 (tp-100) REVERT: B 428 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7884 (ptm160) REVERT: B 431 LYS cc_start: 0.9229 (tttt) cc_final: 0.8962 (ttpt) REVERT: B 578 CYS cc_start: 0.8893 (m) cc_final: 0.8625 (m) REVERT: B 628 ASN cc_start: 0.7683 (t0) cc_final: 0.7108 (t0) REVERT: B 656 LYS cc_start: 0.8891 (tttt) cc_final: 0.8609 (ttpt) REVERT: B 660 ILE cc_start: 0.9545 (tp) cc_final: 0.9305 (tp) REVERT: B 678 LEU cc_start: 0.9391 (tp) cc_final: 0.9158 (tp) REVERT: C 202 GLN cc_start: 0.8248 (tt0) cc_final: 0.7914 (tm-30) REVERT: C 213 ASN cc_start: 0.8914 (t0) cc_final: 0.8517 (t0) REVERT: C 216 LEU cc_start: 0.9249 (mt) cc_final: 0.9002 (mt) REVERT: C 226 ASP cc_start: 0.7671 (t0) cc_final: 0.7430 (t70) REVERT: C 273 GLN cc_start: 0.8045 (tp40) cc_final: 0.7243 (tt0) REVERT: C 274 PRO cc_start: 0.8495 (Cg_endo) cc_final: 0.8227 (Cg_exo) REVERT: C 381 LEU cc_start: 0.8877 (mp) cc_final: 0.8619 (mp) REVERT: C 385 SER cc_start: 0.9433 (t) cc_final: 0.9214 (p) REVERT: C 392 LYS cc_start: 0.8671 (mttt) cc_final: 0.8402 (mtpp) REVERT: C 406 THR cc_start: 0.7770 (m) cc_final: 0.7500 (p) REVERT: C 510 SER cc_start: 0.8135 (m) cc_final: 0.7462 (p) REVERT: C 513 GLU cc_start: 0.8714 (mp0) cc_final: 0.8454 (mp0) REVERT: C 578 CYS cc_start: 0.8961 (m) cc_final: 0.8345 (m) REVERT: C 631 TYR cc_start: 0.8655 (t80) cc_final: 0.8373 (t80) REVERT: C 656 LYS cc_start: 0.8595 (pttt) cc_final: 0.8214 (ttpp) REVERT: C 717 ARG cc_start: 0.6384 (mmp80) cc_final: 0.5890 (mmm160) outliers start: 82 outliers final: 55 residues processed: 778 average time/residue: 0.2640 time to fit residues: 318.0303 Evaluate side-chains 786 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 727 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 733 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 0.1980 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 519 GLN A 652 ASN D 393 ASN D 419 ASN D 519 GLN C 206 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN C 676 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18048 Z= 0.168 Angle : 0.593 12.714 24478 Z= 0.304 Chirality : 0.039 0.167 2748 Planarity : 0.004 0.047 3013 Dihedral : 6.662 75.026 2670 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.76 % Favored : 94.06 % Rotamer: Outliers : 3.22 % Allowed : 19.88 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 2137 helix: 1.55 (0.14), residues: 1328 sheet: -0.40 (0.62), residues: 61 loop : -1.31 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 372 HIS 0.006 0.001 HIS C 410 PHE 0.024 0.001 PHE C 439 TYR 0.024 0.001 TYR A 435 ARG 0.006 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 819 time to evaluate : 2.177 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: A 197 SER cc_start: 0.8111 (p) cc_final: 0.7756 (m) REVERT: A 226 ASP cc_start: 0.7921 (t0) cc_final: 0.7657 (t0) REVERT: A 310 ASN cc_start: 0.9434 (t0) cc_final: 0.9167 (t0) REVERT: A 372 TRP cc_start: 0.8365 (p-90) cc_final: 0.7441 (p-90) REVERT: A 378 HIS cc_start: 0.8119 (p-80) cc_final: 0.7835 (p-80) REVERT: A 397 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 401 TYR cc_start: 0.7885 (m-80) cc_final: 0.7558 (m-80) REVERT: A 411 ASP cc_start: 0.8893 (m-30) cc_final: 0.8484 (t0) REVERT: A 414 LEU cc_start: 0.9226 (mm) cc_final: 0.8949 (mp) REVERT: A 432 ARG cc_start: 0.8551 (mtt90) cc_final: 0.8224 (mtm110) REVERT: A 471 ASP cc_start: 0.9003 (m-30) cc_final: 0.8794 (m-30) REVERT: A 551 ASN cc_start: 0.9366 (m-40) cc_final: 0.9018 (m-40) REVERT: A 597 THR cc_start: 0.9623 (m) cc_final: 0.9399 (p) REVERT: A 654 ASP cc_start: 0.8752 (t0) cc_final: 0.8548 (t0) REVERT: A 675 LEU cc_start: 0.8965 (mt) cc_final: 0.8719 (mm) REVERT: A 703 ILE cc_start: 0.9502 (tp) cc_final: 0.9136 (tp) REVERT: A 707 ASP cc_start: 0.8444 (m-30) cc_final: 0.8003 (m-30) REVERT: D 210 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8343 (pp20) REVERT: D 266 PHE cc_start: 0.9105 (t80) cc_final: 0.8866 (t80) REVERT: D 288 LEU cc_start: 0.9436 (mt) cc_final: 0.9218 (mt) REVERT: D 304 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8292 (p90) REVERT: D 308 MET cc_start: 0.8826 (ttm) cc_final: 0.8554 (ttm) REVERT: D 310 ASN cc_start: 0.9251 (t0) cc_final: 0.8869 (t0) REVERT: D 311 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8853 (mm-30) REVERT: D 326 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8127 (mt-10) REVERT: D 355 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7773 (ttm170) REVERT: D 419 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8999 (m-40) REVERT: D 423 GLN cc_start: 0.8981 (tp40) cc_final: 0.8267 (tp-100) REVERT: D 427 ASP cc_start: 0.8865 (m-30) cc_final: 0.8425 (m-30) REVERT: D 471 ASP cc_start: 0.7988 (m-30) cc_final: 0.7704 (m-30) REVERT: D 479 ILE cc_start: 0.9190 (mt) cc_final: 0.8984 (tp) REVERT: D 494 GLN cc_start: 0.8699 (mt0) cc_final: 0.8450 (mt0) REVERT: D 499 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: D 551 ASN cc_start: 0.9559 (m-40) cc_final: 0.9309 (m-40) REVERT: D 579 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8533 (mtm-85) REVERT: D 582 PHE cc_start: 0.8970 (t80) cc_final: 0.8593 (m-10) REVERT: D 597 THR cc_start: 0.9643 (m) cc_final: 0.9363 (p) REVERT: D 678 LEU cc_start: 0.9280 (tp) cc_final: 0.8940 (tp) REVERT: D 684 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8624 (tm-30) REVERT: D 718 LYS cc_start: 0.8673 (ptmt) cc_final: 0.8231 (ptmm) REVERT: B 213 ASN cc_start: 0.8831 (t0) cc_final: 0.8583 (t0) REVERT: B 216 LEU cc_start: 0.9324 (mt) cc_final: 0.9075 (mt) REVERT: B 250 LEU cc_start: 0.9435 (mm) cc_final: 0.9220 (mm) REVERT: B 254 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9403 (tp) REVERT: B 304 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8315 (p90) REVERT: B 309 TYR cc_start: 0.9150 (t80) cc_final: 0.8732 (t80) REVERT: B 423 GLN cc_start: 0.8931 (tp40) cc_final: 0.8597 (tp-100) REVERT: B 428 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.7910 (ptm160) REVERT: B 431 LYS cc_start: 0.9216 (tttt) cc_final: 0.8938 (ttpt) REVERT: B 490 PHE cc_start: 0.8908 (m-10) cc_final: 0.8705 (m-80) REVERT: B 578 CYS cc_start: 0.8868 (m) cc_final: 0.8638 (m) REVERT: B 628 ASN cc_start: 0.7565 (t0) cc_final: 0.7019 (t0) REVERT: B 656 LYS cc_start: 0.8855 (tttt) cc_final: 0.8584 (ttpt) REVERT: B 660 ILE cc_start: 0.9536 (tp) cc_final: 0.9291 (tp) REVERT: B 678 LEU cc_start: 0.9369 (tp) cc_final: 0.9155 (tp) REVERT: C 202 GLN cc_start: 0.8182 (tt0) cc_final: 0.7871 (tp-100) REVERT: C 213 ASN cc_start: 0.8874 (t0) cc_final: 0.8450 (t0) REVERT: C 216 LEU cc_start: 0.9262 (mt) cc_final: 0.8980 (mt) REVERT: C 226 ASP cc_start: 0.7639 (t0) cc_final: 0.7434 (t70) REVERT: C 273 GLN cc_start: 0.8032 (tp40) cc_final: 0.7255 (tt0) REVERT: C 274 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8261 (Cg_exo) REVERT: C 304 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8234 (p90) REVERT: C 372 TRP cc_start: 0.8001 (p-90) cc_final: 0.7222 (p-90) REVERT: C 392 LYS cc_start: 0.8609 (mttt) cc_final: 0.8331 (mtpp) REVERT: C 397 GLU cc_start: 0.8949 (pt0) cc_final: 0.8469 (pp20) REVERT: C 406 THR cc_start: 0.7665 (m) cc_final: 0.7382 (p) REVERT: C 504 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8046 (tptp) REVERT: C 510 SER cc_start: 0.8196 (m) cc_final: 0.7363 (p) REVERT: C 578 CYS cc_start: 0.8982 (m) cc_final: 0.8355 (m) REVERT: C 631 TYR cc_start: 0.8625 (t80) cc_final: 0.8315 (t80) REVERT: C 656 LYS cc_start: 0.8575 (pttt) cc_final: 0.8322 (tttm) REVERT: C 677 MET cc_start: 0.8744 (ttm) cc_final: 0.8495 (mtp) REVERT: C 709 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: C 717 ARG cc_start: 0.6395 (mmp80) cc_final: 0.6091 (mmm160) outliers start: 61 outliers final: 34 residues processed: 829 average time/residue: 0.2660 time to fit residues: 340.8631 Evaluate side-chains 797 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 755 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.0970 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 652 ASN D 419 ASN C 206 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18048 Z= 0.170 Angle : 0.625 17.500 24478 Z= 0.311 Chirality : 0.040 0.164 2748 Planarity : 0.004 0.048 3013 Dihedral : 6.148 63.382 2670 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 3.22 % Allowed : 22.36 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 2137 helix: 1.53 (0.14), residues: 1316 sheet: -0.45 (0.60), residues: 61 loop : -1.26 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 372 HIS 0.005 0.001 HIS C 410 PHE 0.025 0.001 PHE C 439 TYR 0.026 0.001 TYR A 435 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 762 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 SER cc_start: 0.8061 (p) cc_final: 0.7828 (m) REVERT: A 226 ASP cc_start: 0.7887 (t0) cc_final: 0.7629 (t0) REVERT: A 268 LEU cc_start: 0.8805 (mm) cc_final: 0.8599 (mt) REVERT: A 310 ASN cc_start: 0.9419 (t0) cc_final: 0.9187 (t0) REVERT: A 372 TRP cc_start: 0.8416 (p-90) cc_final: 0.7443 (p-90) REVERT: A 378 HIS cc_start: 0.8061 (p-80) cc_final: 0.7805 (p-80) REVERT: A 397 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 401 TYR cc_start: 0.7805 (m-80) cc_final: 0.7461 (m-80) REVERT: A 411 ASP cc_start: 0.8876 (m-30) cc_final: 0.8629 (t0) REVERT: A 432 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8219 (mtm110) REVERT: A 523 MET cc_start: 0.9516 (tpp) cc_final: 0.9099 (tpp) REVERT: A 551 ASN cc_start: 0.9243 (m-40) cc_final: 0.8961 (m-40) REVERT: A 597 THR cc_start: 0.9607 (m) cc_final: 0.9390 (p) REVERT: A 703 ILE cc_start: 0.9510 (tp) cc_final: 0.9139 (tp) REVERT: A 707 ASP cc_start: 0.8435 (m-30) cc_final: 0.7999 (m-30) REVERT: D 210 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8350 (pp20) REVERT: D 250 LEU cc_start: 0.9252 (mm) cc_final: 0.9000 (mt) REVERT: D 266 PHE cc_start: 0.9120 (t80) cc_final: 0.8879 (t80) REVERT: D 288 LEU cc_start: 0.9445 (mt) cc_final: 0.9228 (mt) REVERT: D 304 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8247 (p90) REVERT: D 308 MET cc_start: 0.8814 (ttm) cc_final: 0.8521 (ttm) REVERT: D 310 ASN cc_start: 0.9237 (t0) cc_final: 0.8890 (t0) REVERT: D 311 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8864 (mm-30) REVERT: D 326 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8039 (mt-10) REVERT: D 355 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7755 (ttm170) REVERT: D 356 GLU cc_start: 0.7966 (tt0) cc_final: 0.7599 (tm-30) REVERT: D 423 GLN cc_start: 0.8961 (tp40) cc_final: 0.8238 (tp-100) REVERT: D 427 ASP cc_start: 0.8862 (m-30) cc_final: 0.8419 (m-30) REVERT: D 471 ASP cc_start: 0.7949 (m-30) cc_final: 0.7676 (m-30) REVERT: D 479 ILE cc_start: 0.9206 (mt) cc_final: 0.8982 (tp) REVERT: D 494 GLN cc_start: 0.8686 (mt0) cc_final: 0.8412 (mt0) REVERT: D 499 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7538 (mmm-85) REVERT: D 582 PHE cc_start: 0.8977 (t80) cc_final: 0.8577 (m-10) REVERT: D 660 ILE cc_start: 0.9688 (tp) cc_final: 0.9454 (tp) REVERT: D 692 GLU cc_start: 0.8248 (mp0) cc_final: 0.8046 (mp0) REVERT: D 697 TRP cc_start: 0.8760 (t60) cc_final: 0.8503 (t60) REVERT: D 718 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8232 (ptmm) REVERT: B 211 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7338 (mtt180) REVERT: B 213 ASN cc_start: 0.8811 (t0) cc_final: 0.8594 (t0) REVERT: B 216 LEU cc_start: 0.9321 (mt) cc_final: 0.9075 (mt) REVERT: B 250 LEU cc_start: 0.9453 (mm) cc_final: 0.9229 (mm) REVERT: B 254 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9422 (tp) REVERT: B 423 GLN cc_start: 0.8912 (tp40) cc_final: 0.8383 (tp-100) REVERT: B 428 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.7993 (ptm160) REVERT: B 431 LYS cc_start: 0.9203 (tttt) cc_final: 0.8937 (ttpp) REVERT: B 490 PHE cc_start: 0.8890 (m-10) cc_final: 0.8690 (m-80) REVERT: B 491 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8885 (ttm-80) REVERT: B 575 ARG cc_start: 0.8635 (mtt180) cc_final: 0.8228 (mmt180) REVERT: B 578 CYS cc_start: 0.8886 (m) cc_final: 0.8681 (m) REVERT: B 628 ASN cc_start: 0.7471 (t0) cc_final: 0.7229 (t0) REVERT: B 656 LYS cc_start: 0.8870 (tttt) cc_final: 0.8619 (ttpt) REVERT: B 660 ILE cc_start: 0.9527 (tp) cc_final: 0.9276 (tp) REVERT: B 678 LEU cc_start: 0.9348 (tp) cc_final: 0.9131 (tp) REVERT: C 202 GLN cc_start: 0.8163 (tt0) cc_final: 0.7849 (tp-100) REVERT: C 213 ASN cc_start: 0.8927 (t0) cc_final: 0.8501 (t0) REVERT: C 216 LEU cc_start: 0.9283 (mt) cc_final: 0.9046 (mt) REVERT: C 226 ASP cc_start: 0.7684 (t0) cc_final: 0.7458 (t70) REVERT: C 273 GLN cc_start: 0.8001 (tp40) cc_final: 0.7220 (tt0) REVERT: C 274 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8255 (Cg_exo) REVERT: C 304 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (p90) REVERT: C 308 MET cc_start: 0.8956 (tpp) cc_final: 0.8645 (tpp) REVERT: C 368 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8073 (ttpt) REVERT: C 372 TRP cc_start: 0.8023 (p-90) cc_final: 0.7315 (p-90) REVERT: C 392 LYS cc_start: 0.8673 (mttt) cc_final: 0.8399 (mtpp) REVERT: C 397 GLU cc_start: 0.8968 (pt0) cc_final: 0.8470 (pp20) REVERT: C 406 THR cc_start: 0.7640 (m) cc_final: 0.7439 (p) REVERT: C 445 MET cc_start: 0.9465 (mmm) cc_final: 0.9222 (mmm) REVERT: C 504 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7993 (tptp) REVERT: C 578 CYS cc_start: 0.8999 (m) cc_final: 0.8627 (m) REVERT: C 631 TYR cc_start: 0.8598 (t80) cc_final: 0.8290 (t80) REVERT: C 653 TYR cc_start: 0.7978 (p90) cc_final: 0.7619 (p90) REVERT: C 656 LYS cc_start: 0.8625 (pttt) cc_final: 0.8270 (tttp) REVERT: C 688 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8723 (tppt) REVERT: C 708 THR cc_start: 0.9659 (m) cc_final: 0.9441 (t) REVERT: C 709 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8505 (tt0) outliers start: 61 outliers final: 38 residues processed: 781 average time/residue: 0.2759 time to fit residues: 334.8479 Evaluate side-chains 770 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 726 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 560 GLN A 652 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18048 Z= 0.180 Angle : 0.622 17.419 24478 Z= 0.311 Chirality : 0.040 0.217 2748 Planarity : 0.004 0.049 3013 Dihedral : 5.666 53.136 2670 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.59 % Allowed : 23.05 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2137 helix: 1.56 (0.14), residues: 1297 sheet: -0.33 (0.60), residues: 61 loop : -1.21 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 372 HIS 0.005 0.001 HIS A 410 PHE 0.021 0.001 PHE C 439 TYR 0.027 0.001 TYR A 435 ARG 0.014 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 745 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7882 (t0) cc_final: 0.7623 (t0) REVERT: A 268 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8581 (mt) REVERT: A 372 TRP cc_start: 0.8415 (p-90) cc_final: 0.7461 (p-90) REVERT: A 378 HIS cc_start: 0.8021 (p-80) cc_final: 0.7818 (p-80) REVERT: A 397 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8204 (tm-30) REVERT: A 401 TYR cc_start: 0.7819 (m-80) cc_final: 0.7483 (m-80) REVERT: A 411 ASP cc_start: 0.8852 (m-30) cc_final: 0.8597 (t0) REVERT: A 420 ARG cc_start: 0.8748 (mtt-85) cc_final: 0.8511 (mtt-85) REVERT: A 432 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8220 (mtm110) REVERT: A 551 ASN cc_start: 0.9192 (m-40) cc_final: 0.8908 (m-40) REVERT: A 597 THR cc_start: 0.9604 (m) cc_final: 0.9395 (p) REVERT: A 688 LYS cc_start: 0.8666 (mttt) cc_final: 0.8451 (ptpt) REVERT: A 703 ILE cc_start: 0.9511 (tp) cc_final: 0.9137 (tp) REVERT: A 707 ASP cc_start: 0.8437 (m-30) cc_final: 0.8011 (m-30) REVERT: D 210 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8318 (pp20) REVERT: D 250 LEU cc_start: 0.9221 (mm) cc_final: 0.8964 (mt) REVERT: D 288 LEU cc_start: 0.9423 (mt) cc_final: 0.9196 (mt) REVERT: D 304 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8198 (p90) REVERT: D 308 MET cc_start: 0.8786 (ttm) cc_final: 0.8454 (ttm) REVERT: D 310 ASN cc_start: 0.9250 (t0) cc_final: 0.8919 (t0) REVERT: D 311 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8885 (mm-30) REVERT: D 356 GLU cc_start: 0.7959 (tt0) cc_final: 0.7631 (tm-30) REVERT: D 471 ASP cc_start: 0.7963 (m-30) cc_final: 0.7697 (m-30) REVERT: D 479 ILE cc_start: 0.9204 (mt) cc_final: 0.8967 (tp) REVERT: D 494 GLN cc_start: 0.8650 (mt0) cc_final: 0.8408 (mt0) REVERT: D 582 PHE cc_start: 0.9005 (t80) cc_final: 0.8582 (m-10) REVERT: D 697 TRP cc_start: 0.8795 (t60) cc_final: 0.8552 (t60) REVERT: D 718 LYS cc_start: 0.8644 (ptmt) cc_final: 0.8265 (ptmm) REVERT: B 213 ASN cc_start: 0.8801 (t0) cc_final: 0.8594 (t0) REVERT: B 216 LEU cc_start: 0.9323 (mt) cc_final: 0.9081 (mt) REVERT: B 250 LEU cc_start: 0.9427 (mm) cc_final: 0.9209 (mm) REVERT: B 423 GLN cc_start: 0.8919 (tp40) cc_final: 0.8394 (tp-100) REVERT: B 428 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.7984 (ptm160) REVERT: B 431 LYS cc_start: 0.9196 (tttt) cc_final: 0.8945 (ttpp) REVERT: B 575 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8268 (mmt180) REVERT: B 578 CYS cc_start: 0.8888 (m) cc_final: 0.8678 (m) REVERT: B 628 ASN cc_start: 0.7507 (t0) cc_final: 0.7007 (t0) REVERT: B 656 LYS cc_start: 0.8886 (tttt) cc_final: 0.8589 (ttpt) REVERT: B 660 ILE cc_start: 0.9490 (tp) cc_final: 0.9255 (tp) REVERT: C 202 GLN cc_start: 0.8142 (tt0) cc_final: 0.7817 (tp-100) REVERT: C 213 ASN cc_start: 0.8915 (t0) cc_final: 0.8499 (t0) REVERT: C 216 LEU cc_start: 0.9306 (mt) cc_final: 0.9046 (mt) REVERT: C 226 ASP cc_start: 0.7698 (t0) cc_final: 0.7199 (t70) REVERT: C 304 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8339 (p90) REVERT: C 308 MET cc_start: 0.8973 (tpp) cc_final: 0.8680 (tpp) REVERT: C 368 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8253 (ttpt) REVERT: C 372 TRP cc_start: 0.8043 (p-90) cc_final: 0.7132 (p-90) REVERT: C 392 LYS cc_start: 0.8668 (mttt) cc_final: 0.8386 (mtpp) REVERT: C 397 GLU cc_start: 0.9000 (pt0) cc_final: 0.8511 (pp20) REVERT: C 445 MET cc_start: 0.9410 (mmm) cc_final: 0.9205 (mmm) REVERT: C 504 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7947 (tptp) REVERT: C 578 CYS cc_start: 0.9013 (m) cc_final: 0.8606 (m) REVERT: C 631 TYR cc_start: 0.8597 (t80) cc_final: 0.8342 (t80) REVERT: C 653 TYR cc_start: 0.7862 (p90) cc_final: 0.7622 (p90) REVERT: C 656 LYS cc_start: 0.8652 (pttt) cc_final: 0.8327 (tttp) REVERT: C 664 LEU cc_start: 0.9697 (mp) cc_final: 0.9462 (mp) REVERT: C 688 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8778 (tppt) REVERT: C 709 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: C 740 TRP cc_start: 0.8456 (m100) cc_final: 0.7908 (m100) outliers start: 68 outliers final: 49 residues processed: 764 average time/residue: 0.2698 time to fit residues: 316.3758 Evaluate side-chains 773 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 718 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 172 optimal weight: 0.0670 chunk 114 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS D 519 GLN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18048 Z= 0.312 Angle : 0.668 13.379 24478 Z= 0.340 Chirality : 0.042 0.204 2748 Planarity : 0.004 0.054 3013 Dihedral : 5.566 48.227 2670 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 4.38 % Allowed : 22.78 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2137 helix: 1.51 (0.14), residues: 1290 sheet: -0.36 (0.58), residues: 61 loop : -1.21 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 372 HIS 0.004 0.001 HIS A 320 PHE 0.020 0.002 PHE C 439 TYR 0.027 0.001 TYR A 435 ARG 0.006 0.001 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 704 time to evaluate : 1.951 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: A 226 ASP cc_start: 0.7907 (t0) cc_final: 0.7658 (t0) REVERT: A 372 TRP cc_start: 0.8443 (p-90) cc_final: 0.7352 (p-90) REVERT: A 378 HIS cc_start: 0.8071 (p-80) cc_final: 0.7867 (p-80) REVERT: A 411 ASP cc_start: 0.8830 (m-30) cc_final: 0.8606 (t0) REVERT: A 420 ARG cc_start: 0.8787 (mtt-85) cc_final: 0.8546 (mtt-85) REVERT: A 432 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8272 (mtm110) REVERT: A 438 PHE cc_start: 0.8941 (t80) cc_final: 0.8704 (t80) REVERT: A 551 ASN cc_start: 0.9198 (m-40) cc_final: 0.8903 (m-40) REVERT: A 703 ILE cc_start: 0.9521 (tp) cc_final: 0.9162 (tp) REVERT: A 707 ASP cc_start: 0.8459 (m-30) cc_final: 0.8001 (m-30) REVERT: A 749 TRP cc_start: 0.7791 (m-90) cc_final: 0.7549 (m-90) REVERT: D 234 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8076 (p0) REVERT: D 288 LEU cc_start: 0.9462 (mt) cc_final: 0.9240 (mt) REVERT: D 304 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8184 (p90) REVERT: D 308 MET cc_start: 0.8812 (ttm) cc_final: 0.8505 (ttm) REVERT: D 310 ASN cc_start: 0.9305 (t0) cc_final: 0.8929 (t0) REVERT: D 311 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8876 (mm-30) REVERT: D 356 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: D 471 ASP cc_start: 0.8065 (m-30) cc_final: 0.7808 (m-30) REVERT: D 494 GLN cc_start: 0.8660 (mt0) cc_final: 0.8351 (mm-40) REVERT: D 582 PHE cc_start: 0.9043 (t80) cc_final: 0.8564 (m-10) REVERT: D 697 TRP cc_start: 0.8936 (t60) cc_final: 0.8641 (t60) REVERT: D 718 LYS cc_start: 0.8705 (ptmt) cc_final: 0.8340 (ptmm) REVERT: B 285 ASN cc_start: 0.9269 (m-40) cc_final: 0.8984 (m110) REVERT: B 423 GLN cc_start: 0.8959 (tp40) cc_final: 0.8602 (tp-100) REVERT: B 428 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8016 (ptm160) REVERT: B 431 LYS cc_start: 0.9235 (tttt) cc_final: 0.8976 (ttpt) REVERT: B 491 ARG cc_start: 0.9153 (ttm-80) cc_final: 0.8853 (ttm-80) REVERT: B 564 ILE cc_start: 0.8808 (mm) cc_final: 0.8352 (mm) REVERT: B 575 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8286 (mmt180) REVERT: B 578 CYS cc_start: 0.8936 (m) cc_final: 0.8730 (m) REVERT: B 628 ASN cc_start: 0.7531 (t0) cc_final: 0.7075 (t0) REVERT: B 656 LYS cc_start: 0.8912 (tttt) cc_final: 0.8585 (ttpp) REVERT: B 660 ILE cc_start: 0.9510 (tp) cc_final: 0.9272 (tp) REVERT: C 202 GLN cc_start: 0.8211 (tt0) cc_final: 0.7830 (tp-100) REVERT: C 213 ASN cc_start: 0.8985 (t0) cc_final: 0.8540 (t0) REVERT: C 216 LEU cc_start: 0.9317 (mt) cc_final: 0.9039 (mt) REVERT: C 226 ASP cc_start: 0.7733 (t0) cc_final: 0.7277 (t70) REVERT: C 368 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8313 (ttpt) REVERT: C 372 TRP cc_start: 0.7929 (p-90) cc_final: 0.7019 (p-90) REVERT: C 392 LYS cc_start: 0.8673 (mttt) cc_final: 0.8388 (mtpp) REVERT: C 513 GLU cc_start: 0.8706 (mp0) cc_final: 0.8446 (pm20) REVERT: C 554 TYR cc_start: 0.9259 (t80) cc_final: 0.8987 (t80) REVERT: C 578 CYS cc_start: 0.9035 (m) cc_final: 0.8618 (m) REVERT: C 653 TYR cc_start: 0.8248 (p90) cc_final: 0.7948 (p90) REVERT: C 656 LYS cc_start: 0.8714 (pttt) cc_final: 0.8388 (tttp) REVERT: C 688 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8790 (tppt) REVERT: C 700 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8508 (tm-30) outliers start: 83 outliers final: 59 residues processed: 729 average time/residue: 0.2672 time to fit residues: 301.0935 Evaluate side-chains 736 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 674 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 696 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 160 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 GLN C 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18048 Z= 0.174 Angle : 0.683 15.554 24478 Z= 0.335 Chirality : 0.042 0.320 2748 Planarity : 0.004 0.072 3013 Dihedral : 5.251 43.092 2670 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.85 % Allowed : 25.74 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2137 helix: 1.40 (0.14), residues: 1287 sheet: -0.22 (0.60), residues: 61 loop : -1.20 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 372 HIS 0.004 0.001 HIS B 358 PHE 0.028 0.001 PHE A 266 TYR 0.017 0.001 TYR B 246 ARG 0.006 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 740 time to evaluate : 2.032 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: A 226 ASP cc_start: 0.7858 (t0) cc_final: 0.7607 (t0) REVERT: A 247 PHE cc_start: 0.8154 (p90) cc_final: 0.7785 (p90) REVERT: A 372 TRP cc_start: 0.8433 (p-90) cc_final: 0.7392 (p-90) REVERT: A 401 TYR cc_start: 0.7843 (m-80) cc_final: 0.7558 (m-80) REVERT: A 420 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.8545 (mtt-85) REVERT: A 432 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8220 (mtm110) REVERT: A 551 ASN cc_start: 0.9107 (m-40) cc_final: 0.8904 (m-40) REVERT: A 684 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8655 (tp30) REVERT: A 703 ILE cc_start: 0.9501 (tp) cc_final: 0.9107 (tp) REVERT: A 707 ASP cc_start: 0.8377 (m-30) cc_final: 0.7963 (m-30) REVERT: D 234 ASP cc_start: 0.8594 (m-30) cc_final: 0.7974 (p0) REVERT: D 288 LEU cc_start: 0.9425 (mt) cc_final: 0.9185 (mt) REVERT: D 304 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8043 (p90) REVERT: D 308 MET cc_start: 0.8771 (ttm) cc_final: 0.8429 (ttm) REVERT: D 310 ASN cc_start: 0.9231 (t0) cc_final: 0.8896 (t0) REVERT: D 311 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8913 (mm-30) REVERT: D 356 GLU cc_start: 0.7914 (tt0) cc_final: 0.7603 (tm-30) REVERT: D 471 ASP cc_start: 0.7991 (m-30) cc_final: 0.7747 (m-30) REVERT: D 582 PHE cc_start: 0.9002 (t80) cc_final: 0.8514 (m-10) REVERT: D 697 TRP cc_start: 0.8804 (t60) cc_final: 0.8563 (t60) REVERT: D 718 LYS cc_start: 0.8641 (ptmt) cc_final: 0.8274 (ptmm) REVERT: B 249 GLU cc_start: 0.7479 (mp0) cc_final: 0.7247 (mp0) REVERT: B 250 LEU cc_start: 0.9448 (mm) cc_final: 0.9172 (mm) REVERT: B 423 GLN cc_start: 0.8946 (tp40) cc_final: 0.8428 (tp-100) REVERT: B 557 ARG cc_start: 0.8866 (mtp180) cc_final: 0.8558 (mtp180) REVERT: B 562 MET cc_start: 0.8722 (mmm) cc_final: 0.8086 (mpp) REVERT: B 575 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8240 (mmt180) REVERT: B 628 ASN cc_start: 0.7392 (t0) cc_final: 0.6904 (t0) REVERT: B 656 LYS cc_start: 0.8881 (tttt) cc_final: 0.8563 (ttpp) REVERT: B 660 ILE cc_start: 0.9475 (tp) cc_final: 0.9240 (tp) REVERT: C 202 GLN cc_start: 0.8145 (tt0) cc_final: 0.7789 (tp-100) REVERT: C 213 ASN cc_start: 0.8928 (t0) cc_final: 0.8516 (t0) REVERT: C 216 LEU cc_start: 0.9350 (mt) cc_final: 0.9067 (mt) REVERT: C 226 ASP cc_start: 0.7754 (t0) cc_final: 0.7344 (t70) REVERT: C 304 PHE cc_start: 0.8515 (p90) cc_final: 0.8005 (p90) REVERT: C 372 TRP cc_start: 0.7938 (p-90) cc_final: 0.7052 (p-90) REVERT: C 392 LYS cc_start: 0.8581 (mttt) cc_final: 0.8294 (mtpp) REVERT: C 497 LEU cc_start: 0.8953 (mp) cc_final: 0.8634 (pp) REVERT: C 513 GLU cc_start: 0.8683 (mp0) cc_final: 0.8425 (pm20) REVERT: C 531 PHE cc_start: 0.8749 (m-80) cc_final: 0.8413 (m-80) REVERT: C 578 CYS cc_start: 0.9030 (m) cc_final: 0.8616 (m) REVERT: C 656 LYS cc_start: 0.8644 (pttt) cc_final: 0.8255 (ttpp) REVERT: C 688 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8800 (tppt) REVERT: C 700 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 709 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 54 outliers final: 37 residues processed: 756 average time/residue: 0.2773 time to fit residues: 324.9992 Evaluate side-chains 753 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 714 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 180 optimal weight: 0.0570 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN A 228 GLN A 410 HIS ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18048 Z= 0.186 Angle : 0.713 16.643 24478 Z= 0.348 Chirality : 0.043 0.386 2748 Planarity : 0.004 0.065 3013 Dihedral : 5.196 44.492 2670 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.22 % Allowed : 27.64 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2137 helix: 1.22 (0.14), residues: 1286 sheet: -0.19 (0.58), residues: 61 loop : -1.25 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 749 HIS 0.007 0.001 HIS A 410 PHE 0.032 0.001 PHE C 369 TYR 0.015 0.001 TYR A 309 ARG 0.011 0.001 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 744 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 SER cc_start: 0.8002 (p) cc_final: 0.7783 (m) REVERT: A 226 ASP cc_start: 0.7783 (t0) cc_final: 0.7553 (t0) REVERT: A 247 PHE cc_start: 0.8164 (p90) cc_final: 0.7829 (p90) REVERT: A 372 TRP cc_start: 0.8456 (p-90) cc_final: 0.7369 (p-90) REVERT: A 397 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 401 TYR cc_start: 0.7830 (m-80) cc_final: 0.7446 (m-80) REVERT: A 432 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8167 (mtm110) REVERT: A 445 MET cc_start: 0.9398 (tpp) cc_final: 0.9112 (mpp) REVERT: A 551 ASN cc_start: 0.9140 (m-40) cc_final: 0.8883 (m-40) REVERT: A 703 ILE cc_start: 0.9472 (tp) cc_final: 0.9070 (tp) REVERT: A 707 ASP cc_start: 0.8373 (m-30) cc_final: 0.7978 (m-30) REVERT: D 211 ARG cc_start: 0.8850 (mmm160) cc_final: 0.8592 (mmm160) REVERT: D 288 LEU cc_start: 0.9427 (mt) cc_final: 0.9188 (mt) REVERT: D 304 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8231 (p90) REVERT: D 308 MET cc_start: 0.8759 (ttm) cc_final: 0.8428 (ttm) REVERT: D 310 ASN cc_start: 0.9217 (t0) cc_final: 0.8902 (t0) REVERT: D 311 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8907 (mm-30) REVERT: D 356 GLU cc_start: 0.7901 (tt0) cc_final: 0.7597 (tm-30) REVERT: D 471 ASP cc_start: 0.7966 (m-30) cc_final: 0.7724 (m-30) REVERT: D 582 PHE cc_start: 0.9021 (t80) cc_final: 0.8478 (m-10) REVERT: D 697 TRP cc_start: 0.8812 (t60) cc_final: 0.8589 (t60) REVERT: D 718 LYS cc_start: 0.8619 (ptmt) cc_final: 0.8287 (ptmm) REVERT: B 249 GLU cc_start: 0.7566 (mp0) cc_final: 0.7263 (mp0) REVERT: B 285 ASN cc_start: 0.9227 (m-40) cc_final: 0.8667 (m110) REVERT: B 562 MET cc_start: 0.8680 (mmm) cc_final: 0.8098 (mpp) REVERT: B 572 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8107 (mpp) REVERT: B 575 ARG cc_start: 0.8583 (mtt180) cc_final: 0.8235 (mmt180) REVERT: B 628 ASN cc_start: 0.7378 (t0) cc_final: 0.6908 (t0) REVERT: B 656 LYS cc_start: 0.8896 (tttt) cc_final: 0.8603 (ttpp) REVERT: B 660 ILE cc_start: 0.9480 (tp) cc_final: 0.9240 (tp) REVERT: B 677 MET cc_start: 0.8770 (mtp) cc_final: 0.8560 (mmm) REVERT: B 718 LYS cc_start: 0.8789 (pttt) cc_final: 0.7958 (pttm) REVERT: C 202 GLN cc_start: 0.8114 (tt0) cc_final: 0.7754 (tp-100) REVERT: C 213 ASN cc_start: 0.8932 (t0) cc_final: 0.8477 (t0) REVERT: C 216 LEU cc_start: 0.9347 (mt) cc_final: 0.9018 (mt) REVERT: C 226 ASP cc_start: 0.7725 (t0) cc_final: 0.7306 (t70) REVERT: C 234 ASP cc_start: 0.8937 (m-30) cc_final: 0.8554 (m-30) REVERT: C 276 ASP cc_start: 0.8596 (t0) cc_final: 0.8155 (t0) REVERT: C 304 PHE cc_start: 0.8611 (p90) cc_final: 0.8194 (p90) REVERT: C 372 TRP cc_start: 0.7928 (p-90) cc_final: 0.7038 (p-90) REVERT: C 392 LYS cc_start: 0.8587 (mttt) cc_final: 0.8322 (mtpp) REVERT: C 445 MET cc_start: 0.9259 (mmm) cc_final: 0.8994 (mmm) REVERT: C 497 LEU cc_start: 0.8921 (mp) cc_final: 0.8620 (pp) REVERT: C 513 GLU cc_start: 0.8673 (mp0) cc_final: 0.8411 (pm20) REVERT: C 554 TYR cc_start: 0.9265 (t80) cc_final: 0.8942 (t80) REVERT: C 578 CYS cc_start: 0.9022 (m) cc_final: 0.8594 (m) REVERT: C 653 TYR cc_start: 0.7766 (p90) cc_final: 0.7345 (p90) REVERT: C 656 LYS cc_start: 0.8648 (pttt) cc_final: 0.8376 (tttp) REVERT: C 688 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8799 (tppt) REVERT: C 700 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8359 (tm-30) outliers start: 42 outliers final: 38 residues processed: 755 average time/residue: 0.2718 time to fit residues: 318.1805 Evaluate side-chains 747 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 707 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 696 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18048 Z= 0.222 Angle : 0.731 15.020 24478 Z= 0.359 Chirality : 0.043 0.451 2748 Planarity : 0.004 0.064 3013 Dihedral : 5.152 44.513 2670 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.32 % Allowed : 28.69 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2137 helix: 1.14 (0.14), residues: 1287 sheet: -0.29 (0.60), residues: 61 loop : -1.31 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 749 HIS 0.014 0.001 HIS A 410 PHE 0.022 0.001 PHE C 369 TYR 0.015 0.001 TYR A 435 ARG 0.008 0.001 ARG D 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 705 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7788 (t0) cc_final: 0.7533 (t0) REVERT: A 247 PHE cc_start: 0.8166 (p90) cc_final: 0.7858 (p90) REVERT: A 372 TRP cc_start: 0.8481 (p-90) cc_final: 0.7345 (p-90) REVERT: A 397 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8076 (tm-30) REVERT: A 398 VAL cc_start: 0.9532 (t) cc_final: 0.9298 (p) REVERT: A 401 TYR cc_start: 0.7862 (m-80) cc_final: 0.7286 (m-80) REVERT: A 432 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8203 (mtm110) REVERT: A 551 ASN cc_start: 0.9181 (m-40) cc_final: 0.8855 (m-40) REVERT: A 703 ILE cc_start: 0.9447 (tp) cc_final: 0.9027 (tp) REVERT: A 707 ASP cc_start: 0.8310 (m-30) cc_final: 0.7876 (m-30) REVERT: D 211 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8569 (mmm160) REVERT: D 234 ASP cc_start: 0.8553 (m-30) cc_final: 0.7980 (p0) REVERT: D 288 LEU cc_start: 0.9446 (mt) cc_final: 0.9212 (mt) REVERT: D 304 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8223 (p90) REVERT: D 308 MET cc_start: 0.8776 (ttm) cc_final: 0.8444 (ttm) REVERT: D 310 ASN cc_start: 0.9234 (t0) cc_final: 0.8911 (t0) REVERT: D 311 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8900 (mm-30) REVERT: D 356 GLU cc_start: 0.7916 (tt0) cc_final: 0.7615 (tm-30) REVERT: D 372 TRP cc_start: 0.8314 (p-90) cc_final: 0.7784 (p-90) REVERT: D 471 ASP cc_start: 0.8016 (m-30) cc_final: 0.7772 (m-30) REVERT: D 582 PHE cc_start: 0.9048 (t80) cc_final: 0.8493 (m-10) REVERT: D 697 TRP cc_start: 0.8851 (t60) cc_final: 0.8620 (t60) REVERT: D 718 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8316 (ptmm) REVERT: B 249 GLU cc_start: 0.7584 (mp0) cc_final: 0.7230 (mp0) REVERT: B 267 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9386 (mt) REVERT: B 285 ASN cc_start: 0.9234 (m-40) cc_final: 0.8938 (m110) REVERT: B 562 MET cc_start: 0.8695 (mmm) cc_final: 0.8132 (mpp) REVERT: B 575 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8223 (mmt180) REVERT: B 628 ASN cc_start: 0.7383 (t0) cc_final: 0.6928 (t0) REVERT: B 656 LYS cc_start: 0.8908 (tttt) cc_final: 0.8618 (ttpp) REVERT: B 660 ILE cc_start: 0.9487 (tp) cc_final: 0.9237 (tp) REVERT: C 202 GLN cc_start: 0.8137 (tt0) cc_final: 0.7748 (tp-100) REVERT: C 213 ASN cc_start: 0.8965 (t0) cc_final: 0.8521 (t0) REVERT: C 216 LEU cc_start: 0.9348 (mt) cc_final: 0.9012 (mt) REVERT: C 226 ASP cc_start: 0.7750 (t0) cc_final: 0.7332 (t70) REVERT: C 304 PHE cc_start: 0.8634 (p90) cc_final: 0.8221 (p90) REVERT: C 372 TRP cc_start: 0.7922 (p-90) cc_final: 0.6908 (p-90) REVERT: C 392 LYS cc_start: 0.8632 (mttt) cc_final: 0.8368 (mtpp) REVERT: C 445 MET cc_start: 0.9297 (mmm) cc_final: 0.9052 (mmm) REVERT: C 497 LEU cc_start: 0.8918 (mp) cc_final: 0.8583 (pp) REVERT: C 513 GLU cc_start: 0.8670 (mp0) cc_final: 0.8425 (pm20) REVERT: C 554 TYR cc_start: 0.9266 (t80) cc_final: 0.8932 (t80) REVERT: C 578 CYS cc_start: 0.9012 (m) cc_final: 0.8594 (m) REVERT: C 644 MET cc_start: 0.8678 (mmm) cc_final: 0.8426 (mtp) REVERT: C 653 TYR cc_start: 0.7847 (p90) cc_final: 0.7368 (p90) REVERT: C 656 LYS cc_start: 0.8669 (pttt) cc_final: 0.8286 (pttm) REVERT: C 688 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8827 (tppt) REVERT: C 700 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8325 (tm-30) outliers start: 44 outliers final: 36 residues processed: 718 average time/residue: 0.2629 time to fit residues: 294.3178 Evaluate side-chains 740 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 702 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 696 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 320 HIS ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088210 restraints weight = 43558.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091043 restraints weight = 21088.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092941 restraints weight = 13197.232| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 18048 Z= 0.420 Angle : 0.817 13.955 24478 Z= 0.413 Chirality : 0.048 0.514 2748 Planarity : 0.005 0.054 3013 Dihedral : 5.619 41.360 2670 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 3.06 % Allowed : 28.11 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2137 helix: 0.98 (0.14), residues: 1279 sheet: -0.44 (0.58), residues: 61 loop : -1.44 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 749 HIS 0.014 0.002 HIS A 410 PHE 0.033 0.002 PHE A 266 TYR 0.017 0.002 TYR C 495 ARG 0.008 0.001 ARG D 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5344.74 seconds wall clock time: 97 minutes 4.94 seconds (5824.94 seconds total)