Starting phenix.real_space_refine on Sun Mar 17 19:04:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz9_24086/03_2024/7mz9_24086_updated.pdb" } resolution = 3.18 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= 0.002 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 3 5.49 5 S 105 5.16 5 Na 1 4.78 5 C 12185 2.51 5 N 3000 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 557": "NH1" <-> "NH2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 654": "OD1" <-> "OD2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18640 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4368 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 523} Chain: "D" 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: "C" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5016 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 602} Chain: "B" Number of atoms: 4726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4726 Classifications: {'peptide': 584} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 568} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' NA': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.90, per 1000 atoms: 0.53 Number of scatterers: 18640 At special positions: 0 Unit cell: (125.934, 130.104, 119.262, 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 105 16.00 P 3 15.00 Na 1 11.00 O 3346 8.00 N 3000 7.00 C 12185 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=2.04 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: 7.53 Conformation dependent library (CDL) restraints added in 3.6 seconds 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4316 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 4 sheets defined 57.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 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: 4.123A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.483A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.104A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.214A 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: 3.956A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 4.345A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.041A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.056A 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 674 through 711 removed outlier: 6.137A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) 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 268 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 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 5.155A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.166A 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: 3.956A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.895A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.095A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.172A 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 673 through 688 removed outlier: 3.580A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 711 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 187 through 190 No H-bonds generated for 'chain 'C' and resid 187 through 190' 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 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 removed outlier: 4.023A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) 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 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 453 removed outlier: 5.231A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.157A 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 556 removed outlier: 3.936A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 4.040A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.095A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.014A 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 674 through 688 removed outlier: 3.566A pdb=" N LYS C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 711 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' 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: 3.529A 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: 3.804A 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: 5.352A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.098A 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: 3.846A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.941A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.081A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.128A 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 674 through 688 removed outlier: 3.605A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 4.010A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.447A 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: 3.807A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.926A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.803A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2559 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: 4.90 Time building geometry restraints manager: 8.04 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: 2898 1.30 - 1.43: 5312 1.43 - 1.56: 10690 1.56 - 1.69: 10 1.69 - 1.82: 171 Bond restraints: 19081 Sorted by residual: bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.200 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CAV 6EU A 901 " pdb=" CBB 6EU A 901 " ideal model delta sigma weight residual 1.330 1.521 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" CAL 6EU A 901 " pdb=" OAB 6EU A 901 " ideal model delta sigma weight residual 1.415 1.239 0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" CBG 6EU A 901 " pdb=" CBI 6EU A 901 " ideal model delta sigma weight residual 1.388 1.516 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" CBE 6EU A 901 " pdb=" CBH 6EU A 901 " ideal model delta sigma weight residual 1.392 1.519 -0.127 2.00e-02 2.50e+03 4.03e+01 ... (remaining 19076 not shown) Histogram of bond angle deviations from ideal: 96.37 - 103.90: 208 103.90 - 111.42: 8408 111.42 - 118.95: 6829 118.95 - 126.48: 10168 126.48 - 134.00: 226 Bond angle restraints: 25839 Sorted by residual: angle pdb=" N ASP C 654 " pdb=" CA ASP C 654 " pdb=" C ASP C 654 " ideal model delta sigma weight residual 109.81 100.33 9.48 1.53e+00 4.27e-01 3.84e+01 angle pdb=" N ASP D 654 " pdb=" CA ASP D 654 " pdb=" C ASP D 654 " ideal model delta sigma weight residual 109.81 100.58 9.23 1.53e+00 4.27e-01 3.64e+01 angle pdb=" N SER A 722 " pdb=" CA SER A 722 " pdb=" CB SER A 722 " ideal model delta sigma weight residual 114.17 108.16 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" C SER D 711 " pdb=" N PHE D 712 " pdb=" CA PHE D 712 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 ... (remaining 25834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 11016 23.80 - 47.60: 255 47.60 - 71.39: 49 71.39 - 95.19: 6 95.19 - 118.99: 3 Dihedral angle restraints: 11329 sinusoidal: 4614 harmonic: 6715 Sorted by residual: dihedral pdb=" CA TYR B 653 " pdb=" C TYR B 653 " pdb=" N ASP B 654 " pdb=" CA ASP B 654 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+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 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE B 429 " pdb=" C PHE B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 11326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.022: 2908 1.022 - 2.045: 0 2.045 - 3.067: 0 3.067 - 4.090: 0 4.090 - 5.112: 6 Chirality restraints: 2914 Sorted by residual: chirality pdb=" C3 XJ7 B 801 " pdb=" C2 XJ7 B 801 " pdb=" C24 XJ7 B 801 " pdb=" O3 XJ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.61 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C3 XJ7 C 801 " pdb=" C2 XJ7 C 801 " pdb=" C24 XJ7 C 801 " pdb=" O3 XJ7 C 801 " both_signs ideal model delta sigma weight residual False -2.50 2.61 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C3 XJ7 D 801 " pdb=" C2 XJ7 D 801 " pdb=" C24 XJ7 D 801 " pdb=" O3 XJ7 D 801 " both_signs ideal model delta sigma weight residual False -2.50 2.60 -5.11 2.00e-01 2.50e+01 6.52e+02 ... (remaining 2911 not shown) Planarity restraints: 3192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " -0.098 2.00e-02 2.50e+03 1.72e-01 2.97e+02 pdb=" CAV 6EU A 901 " 0.299 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " -0.100 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C GLY B 548 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY B 548 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP B 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 543 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C PHE B 543 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE B 543 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 544 " -0.015 2.00e-02 2.50e+03 ... (remaining 3189 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 234 2.63 - 3.20: 18290 3.20 - 3.77: 28816 3.77 - 4.33: 40496 4.33 - 4.90: 67133 Nonbonded interactions: 154969 Sorted by model distance: nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.069 2.440 nonbonded pdb=" OE2 GLU D 570 " pdb=" O11 XJ7 D 801 " model vdw 2.172 2.440 nonbonded pdb=" OE2 GLU C 416 " pdb=" NE ARG C 420 " model vdw 2.248 2.520 nonbonded pdb=" OE2 GLU B 416 " pdb=" NE ARG B 420 " model vdw 2.254 2.520 nonbonded pdb=" N GLU C 458 " pdb=" OE1 GLU C 458 " model vdw 2.258 2.520 ... (remaining 154964 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 193 through 752) selection = (chain 'B' and resid 193 through 752) selection = (chain 'C' and resid 193 through 752) selection = (chain 'D' and resid 193 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.010 Extract box with map and model: 7.960 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 49.890 Find NCS groups from input model: 1.440 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.010 0.222 19081 Z= 0.652 Angle : 0.828 13.638 25839 Z= 0.449 Chirality : 0.232 5.112 2914 Planarity : 0.006 0.172 3192 Dihedral : 11.713 118.988 7010 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.81 % Favored : 93.96 % Rotamer: Outliers : 0.65 % Allowed : 1.49 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.30 (0.17), residues: 2270 helix: 1.08 (0.13), residues: 1431 sheet: -1.91 (0.48), residues: 71 loop : -1.22 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 749 HIS 0.004 0.001 HIS A 364 PHE 0.028 0.002 PHE A 304 TYR 0.028 0.002 TYR A 511 ARG 0.007 0.001 ARG D 739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 629 time to evaluate : 2.036 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 311 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8547 (mm-30) REVERT: A 409 ARG cc_start: 0.6966 (ptt-90) cc_final: 0.6639 (tmm-80) REVERT: A 496 PHE cc_start: 0.8138 (t80) cc_final: 0.7864 (m-10) REVERT: A 511 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6865 (p90) REVERT: A 569 ILE cc_start: 0.8518 (mt) cc_final: 0.8318 (mt) REVERT: A 570 GLU cc_start: 0.8212 (tt0) cc_final: 0.7777 (tt0) REVERT: A 579 ARG cc_start: 0.8304 (mtm180) cc_final: 0.8082 (mtt-85) REVERT: A 601 ASP cc_start: 0.7412 (t0) cc_final: 0.7203 (t0) REVERT: A 644 MET cc_start: 0.9023 (mmm) cc_final: 0.8473 (mmm) REVERT: D 223 ASN cc_start: 0.8381 (m110) cc_final: 0.8180 (m110) REVERT: D 226 ASP cc_start: 0.7894 (t0) cc_final: 0.7673 (t0) REVERT: D 320 HIS cc_start: 0.8525 (m-70) cc_final: 0.8205 (m-70) REVERT: D 322 THR cc_start: 0.9069 (p) cc_final: 0.8848 (t) REVERT: D 471 ASP cc_start: 0.8531 (m-30) cc_final: 0.8230 (m-30) REVERT: D 504 LYS cc_start: 0.8662 (tttt) cc_final: 0.8205 (ttmt) REVERT: C 166 HIS cc_start: 0.7108 (m-70) cc_final: 0.6821 (m-70) REVERT: C 199 TYR cc_start: 0.6281 (m-80) cc_final: 0.5462 (m-10) REVERT: C 211 ARG cc_start: 0.8719 (mmt-90) cc_final: 0.8476 (mmm160) REVERT: C 234 ASP cc_start: 0.8285 (m-30) cc_final: 0.8019 (m-30) REVERT: C 293 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8313 (mm-30) REVERT: C 304 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8429 (p90) REVERT: C 309 TYR cc_start: 0.9388 (t80) cc_final: 0.9049 (t80) REVERT: C 324 LYS cc_start: 0.8251 (mttt) cc_final: 0.7885 (mttm) REVERT: C 326 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8103 (mt-10) REVERT: C 361 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7175 (mm-30) REVERT: C 384 LEU cc_start: 0.8702 (mp) cc_final: 0.8498 (tt) REVERT: C 386 CYS cc_start: 0.7043 (m) cc_final: 0.6561 (m) REVERT: C 388 ASP cc_start: 0.8198 (t0) cc_final: 0.7898 (t0) REVERT: C 389 THR cc_start: 0.8987 (t) cc_final: 0.8725 (p) REVERT: C 424 ASP cc_start: 0.8888 (t70) cc_final: 0.8635 (t0) REVERT: C 496 PHE cc_start: 0.8543 (t80) cc_final: 0.8083 (m-10) REVERT: C 504 LYS cc_start: 0.8616 (tptt) cc_final: 0.8270 (tptm) REVERT: C 688 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8620 (mtmm) REVERT: B 272 TRP cc_start: 0.8008 (m-90) cc_final: 0.7802 (m-90) REVERT: B 273 GLN cc_start: 0.8131 (tp40) cc_final: 0.7926 (tp-100) REVERT: B 466 LYS cc_start: 0.8424 (mttp) cc_final: 0.8088 (mtmt) REVERT: B 472 TYR cc_start: 0.7596 (m-80) cc_final: 0.7267 (m-10) outliers start: 13 outliers final: 4 residues processed: 634 average time/residue: 0.3367 time to fit residues: 310.0792 Evaluate side-chains 453 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 447 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain B residue 304 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.0970 chunk 170 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 131 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 393 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN A 498 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS D 393 ASN C 202 GLN C 393 ASN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19081 Z= 0.163 Angle : 0.574 9.219 25839 Z= 0.300 Chirality : 0.041 0.326 2914 Planarity : 0.004 0.045 3192 Dihedral : 8.408 98.195 2685 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.59 % Favored : 94.10 % Rotamer: Outliers : 1.84 % Allowed : 8.68 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.82 (0.18), residues: 2270 helix: 1.52 (0.14), residues: 1421 sheet: -1.14 (0.53), residues: 71 loop : -1.12 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 372 HIS 0.003 0.000 HIS D 206 PHE 0.017 0.001 PHE D 304 TYR 0.024 0.001 TYR D 199 ARG 0.007 0.000 ARG D 739 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 516 time to evaluate : 2.190 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 311 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8542 (mm-30) REVERT: A 419 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8037 (m-40) REVERT: A 471 ASP cc_start: 0.8270 (m-30) cc_final: 0.7861 (m-30) REVERT: A 496 PHE cc_start: 0.8109 (t80) cc_final: 0.7903 (m-10) REVERT: A 511 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6858 (p90) REVERT: A 540 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 570 GLU cc_start: 0.8094 (tt0) cc_final: 0.7675 (tt0) REVERT: A 579 ARG cc_start: 0.8329 (mtm180) cc_final: 0.8075 (mtt-85) REVERT: A 601 ASP cc_start: 0.7337 (t0) cc_final: 0.7024 (t0) REVERT: D 223 ASN cc_start: 0.8287 (m110) cc_final: 0.8076 (m110) REVERT: D 320 HIS cc_start: 0.8452 (m-70) cc_final: 0.8217 (m-70) REVERT: D 363 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7877 (tpp80) REVERT: D 374 TYR cc_start: 0.8109 (t80) cc_final: 0.7890 (t80) REVERT: D 378 HIS cc_start: 0.8371 (p-80) cc_final: 0.8106 (p90) REVERT: D 504 LYS cc_start: 0.8612 (tttt) cc_final: 0.8139 (ttmt) REVERT: D 653 TYR cc_start: 0.8423 (p90) cc_final: 0.8158 (p90) REVERT: D 698 LYS cc_start: 0.8865 (mttt) cc_final: 0.8618 (mttm) REVERT: D 725 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8715 (mp) REVERT: C 166 HIS cc_start: 0.7164 (m-70) cc_final: 0.6904 (m-70) REVERT: C 199 TYR cc_start: 0.6382 (m-80) cc_final: 0.5450 (m-10) REVERT: C 211 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.8127 (mmp80) REVERT: C 219 LEU cc_start: 0.9357 (tp) cc_final: 0.9152 (tp) REVERT: C 223 ASN cc_start: 0.8541 (m-40) cc_final: 0.8052 (m-40) REVERT: C 234 ASP cc_start: 0.8157 (m-30) cc_final: 0.7912 (m-30) REVERT: C 293 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8235 (mm-30) REVERT: C 304 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8229 (p90) REVERT: C 389 THR cc_start: 0.8795 (t) cc_final: 0.8561 (p) REVERT: C 445 MET cc_start: 0.9453 (mmm) cc_final: 0.8886 (mmp) REVERT: C 465 LEU cc_start: 0.8933 (tp) cc_final: 0.8585 (tt) REVERT: C 494 GLN cc_start: 0.8182 (mt0) cc_final: 0.7877 (tt0) REVERT: C 496 PHE cc_start: 0.8541 (t80) cc_final: 0.8171 (m-10) REVERT: C 504 LYS cc_start: 0.8646 (tptt) cc_final: 0.8303 (tptm) REVERT: B 291 LEU cc_start: 0.9392 (mt) cc_final: 0.9077 (mt) REVERT: B 445 MET cc_start: 0.9362 (mmm) cc_final: 0.9099 (mmm) REVERT: B 472 TYR cc_start: 0.7644 (m-80) cc_final: 0.7177 (m-10) REVERT: B 496 PHE cc_start: 0.8497 (t80) cc_final: 0.8128 (m-10) REVERT: B 740 TRP cc_start: 0.8212 (m100) cc_final: 0.7939 (m100) outliers start: 37 outliers final: 18 residues processed: 533 average time/residue: 0.3298 time to fit residues: 261.1558 Evaluate side-chains 467 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 444 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 204 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19081 Z= 0.266 Angle : 0.589 11.902 25839 Z= 0.303 Chirality : 0.039 0.294 2914 Planarity : 0.004 0.069 3192 Dihedral : 7.493 84.825 2677 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.04 % Favored : 93.74 % Rotamer: Outliers : 2.43 % Allowed : 10.77 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.90 (0.18), residues: 2270 helix: 1.58 (0.14), residues: 1431 sheet: -0.97 (0.53), residues: 76 loop : -1.13 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 372 HIS 0.005 0.001 HIS A 378 PHE 0.025 0.001 PHE B 720 TYR 0.023 0.001 TYR D 199 ARG 0.011 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 455 time to evaluate : 2.213 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 311 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8570 (mm-30) REVERT: A 419 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: A 471 ASP cc_start: 0.8315 (m-30) cc_final: 0.7872 (m-30) REVERT: A 509 ASP cc_start: 0.7495 (m-30) cc_final: 0.7155 (m-30) REVERT: A 511 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6938 (p90) REVERT: A 540 SER cc_start: 0.9250 (OUTLIER) cc_final: 0.8937 (p) REVERT: A 570 GLU cc_start: 0.8135 (tt0) cc_final: 0.7789 (tt0) REVERT: A 579 ARG cc_start: 0.8343 (mtm180) cc_final: 0.8073 (mtt-85) REVERT: A 644 MET cc_start: 0.9066 (mmm) cc_final: 0.8504 (mmm) REVERT: A 721 ARG cc_start: 0.6611 (mmt180) cc_final: 0.6080 (mmt180) REVERT: D 223 ASN cc_start: 0.8270 (m110) cc_final: 0.8052 (m110) REVERT: D 363 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7800 (tpp80) REVERT: D 378 HIS cc_start: 0.8343 (p-80) cc_final: 0.8102 (p90) REVERT: D 504 LYS cc_start: 0.8560 (tttt) cc_final: 0.8120 (ttmt) REVERT: D 698 LYS cc_start: 0.8881 (mttt) cc_final: 0.8659 (mttm) REVERT: C 166 HIS cc_start: 0.7122 (m-70) cc_final: 0.6883 (m-70) REVERT: C 199 TYR cc_start: 0.6460 (m-80) cc_final: 0.5544 (m-10) REVERT: C 210 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 213 ASN cc_start: 0.8753 (t0) cc_final: 0.8096 (t0) REVERT: C 219 LEU cc_start: 0.9342 (tp) cc_final: 0.9139 (tp) REVERT: C 223 ASN cc_start: 0.8475 (m110) cc_final: 0.8058 (m-40) REVERT: C 293 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8295 (mm-30) REVERT: C 304 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8060 (p90) REVERT: C 427 ASP cc_start: 0.8595 (m-30) cc_final: 0.8389 (m-30) REVERT: C 472 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7329 (t80) REVERT: C 496 PHE cc_start: 0.8626 (t80) cc_final: 0.8201 (m-10) REVERT: C 504 LYS cc_start: 0.8565 (tptt) cc_final: 0.8209 (tptm) REVERT: B 267 LEU cc_start: 0.9460 (mt) cc_final: 0.9258 (mp) REVERT: B 291 LEU cc_start: 0.9421 (mt) cc_final: 0.9097 (mt) REVERT: B 374 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6474 (t80) REVERT: B 472 TYR cc_start: 0.7757 (m-80) cc_final: 0.7292 (m-10) REVERT: B 496 PHE cc_start: 0.8555 (t80) cc_final: 0.8178 (m-10) outliers start: 49 outliers final: 28 residues processed: 481 average time/residue: 0.3123 time to fit residues: 225.4779 Evaluate side-chains 459 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 425 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 741 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19081 Z= 0.181 Angle : 0.546 10.434 25839 Z= 0.284 Chirality : 0.038 0.225 2914 Planarity : 0.004 0.046 3192 Dihedral : 7.100 75.096 2677 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.99 % Favored : 93.74 % Rotamer: Outliers : 2.13 % Allowed : 12.16 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2270 helix: 1.69 (0.14), residues: 1418 sheet: -0.71 (0.54), residues: 76 loop : -1.13 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 740 HIS 0.005 0.001 HIS A 378 PHE 0.032 0.001 PHE B 720 TYR 0.017 0.001 TYR D 374 ARG 0.009 0.000 ARG B 743 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 452 time to evaluate : 2.199 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: A 311 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 419 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: A 471 ASP cc_start: 0.8279 (m-30) cc_final: 0.7813 (m-30) REVERT: A 509 ASP cc_start: 0.7440 (m-30) cc_final: 0.7179 (m-30) REVERT: A 511 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6923 (p90) REVERT: A 540 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 570 GLU cc_start: 0.8048 (tt0) cc_final: 0.7681 (tt0) REVERT: A 579 ARG cc_start: 0.8302 (mtm180) cc_final: 0.8073 (mtt-85) REVERT: A 644 MET cc_start: 0.9008 (mmm) cc_final: 0.8419 (mmm) REVERT: D 223 ASN cc_start: 0.8280 (m110) cc_final: 0.8053 (m110) REVERT: D 363 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7789 (tpp80) REVERT: D 471 ASP cc_start: 0.8130 (m-30) cc_final: 0.7630 (t0) REVERT: D 504 LYS cc_start: 0.8554 (tttt) cc_final: 0.8110 (ttmt) REVERT: D 656 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8727 (tppp) REVERT: D 698 LYS cc_start: 0.8851 (mttt) cc_final: 0.8586 (mttm) REVERT: C 166 HIS cc_start: 0.7176 (m-70) cc_final: 0.6951 (m-70) REVERT: C 199 TYR cc_start: 0.6502 (m-80) cc_final: 0.5623 (m-10) REVERT: C 213 ASN cc_start: 0.8572 (t0) cc_final: 0.8277 (t0) REVERT: C 223 ASN cc_start: 0.8396 (m110) cc_final: 0.8175 (m-40) REVERT: C 293 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8309 (mm-30) REVERT: C 304 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7905 (p90) REVERT: C 471 ASP cc_start: 0.7694 (t70) cc_final: 0.7492 (t0) REVERT: C 472 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7403 (t80) REVERT: C 494 GLN cc_start: 0.8207 (mt0) cc_final: 0.7913 (tt0) REVERT: C 496 PHE cc_start: 0.8576 (t80) cc_final: 0.8225 (m-10) REVERT: C 504 LYS cc_start: 0.8556 (tptt) cc_final: 0.8190 (tptm) REVERT: B 199 TYR cc_start: 0.6260 (m-80) cc_final: 0.6048 (m-80) REVERT: B 291 LEU cc_start: 0.9394 (mt) cc_final: 0.9080 (mt) REVERT: B 374 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6472 (t80) REVERT: B 472 TYR cc_start: 0.7712 (m-80) cc_final: 0.7271 (m-10) REVERT: B 496 PHE cc_start: 0.8556 (t80) cc_final: 0.8210 (m-10) outliers start: 43 outliers final: 27 residues processed: 474 average time/residue: 0.3282 time to fit residues: 237.3637 Evaluate side-chains 454 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 420 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 185 optimal weight: 0.0670 chunk 150 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19081 Z= 0.151 Angle : 0.547 17.369 25839 Z= 0.281 Chirality : 0.038 0.297 2914 Planarity : 0.004 0.047 3192 Dihedral : 6.784 66.554 2677 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 2.38 % Allowed : 13.20 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2270 helix: 1.79 (0.14), residues: 1412 sheet: -0.52 (0.55), residues: 76 loop : -1.12 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 372 HIS 0.005 0.000 HIS A 378 PHE 0.028 0.001 PHE B 720 TYR 0.018 0.001 TYR D 374 ARG 0.006 0.000 ARG B 743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 447 time to evaluate : 2.188 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: A 311 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8587 (mm-30) REVERT: A 419 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (m-40) REVERT: A 471 ASP cc_start: 0.8261 (m-30) cc_final: 0.7756 (m-30) REVERT: A 509 ASP cc_start: 0.7457 (m-30) cc_final: 0.7227 (m-30) REVERT: A 511 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6927 (p90) REVERT: A 540 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8935 (p) REVERT: A 570 GLU cc_start: 0.8021 (tt0) cc_final: 0.7641 (tt0) REVERT: A 579 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8066 (mtt-85) REVERT: A 644 MET cc_start: 0.8966 (mmm) cc_final: 0.8363 (mmm) REVERT: A 721 ARG cc_start: 0.6491 (mmt180) cc_final: 0.5929 (mmt180) REVERT: D 223 ASN cc_start: 0.8270 (m110) cc_final: 0.8029 (m110) REVERT: D 239 THR cc_start: 0.6314 (OUTLIER) cc_final: 0.6114 (m) REVERT: D 363 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7787 (tpp80) REVERT: D 504 LYS cc_start: 0.8533 (tttt) cc_final: 0.8080 (ttmt) REVERT: D 698 LYS cc_start: 0.8858 (mttt) cc_final: 0.8588 (mttm) REVERT: C 199 TYR cc_start: 0.6459 (m-80) cc_final: 0.5594 (m-10) REVERT: C 213 ASN cc_start: 0.8545 (t0) cc_final: 0.8158 (t0) REVERT: C 304 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7846 (p90) REVERT: C 363 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7708 (tpp-160) REVERT: C 472 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7412 (t80) REVERT: C 496 PHE cc_start: 0.8587 (t80) cc_final: 0.8210 (m-10) REVERT: C 504 LYS cc_start: 0.8493 (tptt) cc_final: 0.8132 (tptm) REVERT: B 291 LEU cc_start: 0.9396 (mt) cc_final: 0.9083 (mt) REVERT: B 374 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6419 (t80) REVERT: B 472 TYR cc_start: 0.7735 (m-80) cc_final: 0.7293 (m-10) REVERT: B 496 PHE cc_start: 0.8552 (t80) cc_final: 0.8214 (m-10) outliers start: 48 outliers final: 31 residues processed: 472 average time/residue: 0.2966 time to fit residues: 209.8636 Evaluate side-chains 466 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 428 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 0.0570 chunk 195 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 217 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 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 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN D 206 HIS C 223 ASN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19081 Z= 0.135 Angle : 0.520 12.382 25839 Z= 0.269 Chirality : 0.037 0.264 2914 Planarity : 0.003 0.048 3192 Dihedral : 6.482 66.786 2677 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.30 % Favored : 93.52 % Rotamer: Outliers : 2.38 % Allowed : 13.85 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2270 helix: 1.90 (0.14), residues: 1396 sheet: -0.34 (0.56), residues: 76 loop : -1.12 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 372 HIS 0.004 0.001 HIS A 378 PHE 0.025 0.001 PHE B 720 TYR 0.014 0.001 TYR A 309 ARG 0.006 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 457 time to evaluate : 2.235 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 311 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8590 (mm-30) REVERT: A 419 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: A 471 ASP cc_start: 0.8241 (m-30) cc_final: 0.7741 (m-30) REVERT: A 509 ASP cc_start: 0.7576 (m-30) cc_final: 0.7354 (m-30) REVERT: A 511 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6917 (p90) REVERT: A 540 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8919 (p) REVERT: A 570 GLU cc_start: 0.8027 (tt0) cc_final: 0.7636 (tt0) REVERT: A 579 ARG cc_start: 0.8267 (mtm180) cc_final: 0.8043 (mtt-85) REVERT: A 644 MET cc_start: 0.8930 (mmm) cc_final: 0.8302 (mmm) REVERT: D 211 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8503 (mmp80) REVERT: D 223 ASN cc_start: 0.8212 (m110) cc_final: 0.7953 (m110) REVERT: D 363 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7734 (tpp80) REVERT: D 422 LEU cc_start: 0.9162 (mt) cc_final: 0.8956 (mt) REVERT: D 471 ASP cc_start: 0.8135 (m-30) cc_final: 0.7660 (t0) REVERT: D 504 LYS cc_start: 0.8519 (tttt) cc_final: 0.8064 (ttmt) REVERT: D 592 SER cc_start: 0.9393 (m) cc_final: 0.9178 (m) REVERT: D 698 LYS cc_start: 0.8846 (mttt) cc_final: 0.8535 (mmtt) REVERT: C 199 TYR cc_start: 0.6470 (m-80) cc_final: 0.5612 (m-10) REVERT: C 213 ASN cc_start: 0.8480 (t0) cc_final: 0.8081 (t0) REVERT: C 304 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7771 (p90) REVERT: C 363 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7560 (tpp-160) REVERT: C 472 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 494 GLN cc_start: 0.8124 (mt0) cc_final: 0.7864 (tt0) REVERT: C 496 PHE cc_start: 0.8615 (t80) cc_final: 0.8240 (m-10) REVERT: C 504 LYS cc_start: 0.8535 (tptt) cc_final: 0.8153 (tptm) REVERT: B 374 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6344 (t80) REVERT: B 472 TYR cc_start: 0.7702 (m-80) cc_final: 0.7250 (m-10) REVERT: B 491 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7367 (mmm-85) REVERT: B 496 PHE cc_start: 0.8548 (t80) cc_final: 0.8215 (m-10) outliers start: 48 outliers final: 29 residues processed: 485 average time/residue: 0.2993 time to fit residues: 217.3945 Evaluate side-chains 467 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 432 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 216 optimal weight: 0.6980 chunk 135 optimal weight: 0.0010 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS C 223 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19081 Z= 0.145 Angle : 0.543 17.939 25839 Z= 0.278 Chirality : 0.037 0.282 2914 Planarity : 0.003 0.049 3192 Dihedral : 6.358 73.206 2677 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 2.28 % Allowed : 14.19 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.21 (0.18), residues: 2270 helix: 1.90 (0.14), residues: 1395 sheet: -0.23 (0.56), residues: 76 loop : -1.12 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 372 HIS 0.004 0.000 HIS A 378 PHE 0.026 0.001 PHE B 720 TYR 0.012 0.001 TYR A 309 ARG 0.006 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 445 time to evaluate : 2.172 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 311 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 419 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8182 (m-40) REVERT: A 471 ASP cc_start: 0.8234 (m-30) cc_final: 0.7734 (m-30) REVERT: A 491 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8060 (mmm-85) REVERT: A 511 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6914 (p90) REVERT: A 540 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8912 (p) REVERT: A 570 GLU cc_start: 0.8067 (tt0) cc_final: 0.7636 (tt0) REVERT: A 579 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8054 (mtt-85) REVERT: A 700 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 721 ARG cc_start: 0.6518 (mmt180) cc_final: 0.6138 (mmt180) REVERT: D 211 ARG cc_start: 0.8948 (mmm160) cc_final: 0.8514 (mmp80) REVERT: D 223 ASN cc_start: 0.8184 (m110) cc_final: 0.7922 (m110) REVERT: D 324 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8511 (mtmm) REVERT: D 363 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7736 (tpp80) REVERT: D 422 LEU cc_start: 0.9142 (mt) cc_final: 0.8942 (mt) REVERT: D 471 ASP cc_start: 0.8140 (m-30) cc_final: 0.7746 (t0) REVERT: D 504 LYS cc_start: 0.8513 (tttt) cc_final: 0.8065 (ttmt) REVERT: D 592 SER cc_start: 0.9401 (m) cc_final: 0.9188 (m) REVERT: D 698 LYS cc_start: 0.8840 (mttt) cc_final: 0.8530 (mmtt) REVERT: C 199 TYR cc_start: 0.6435 (m-80) cc_final: 0.5588 (m-10) REVERT: C 213 ASN cc_start: 0.8432 (t0) cc_final: 0.8098 (t0) REVERT: C 304 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7595 (p90) REVERT: C 363 ARG cc_start: 0.7736 (tpp-160) cc_final: 0.7486 (tpp-160) REVERT: C 472 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7441 (t80) REVERT: C 494 GLN cc_start: 0.8122 (mt0) cc_final: 0.7875 (tt0) REVERT: C 496 PHE cc_start: 0.8623 (t80) cc_final: 0.8246 (m-10) REVERT: C 504 LYS cc_start: 0.8532 (tptt) cc_final: 0.7997 (mmtt) REVERT: B 291 LEU cc_start: 0.9366 (mt) cc_final: 0.9054 (mt) REVERT: B 460 LEU cc_start: 0.7762 (mt) cc_final: 0.7551 (pp) REVERT: B 472 TYR cc_start: 0.7709 (m-80) cc_final: 0.7284 (m-10) REVERT: B 496 PHE cc_start: 0.8546 (t80) cc_final: 0.8217 (m-10) outliers start: 46 outliers final: 34 residues processed: 470 average time/residue: 0.3058 time to fit residues: 216.7942 Evaluate side-chains 466 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 427 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 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 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS D 310 ASN C 223 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19081 Z= 0.200 Angle : 0.558 15.617 25839 Z= 0.286 Chirality : 0.038 0.302 2914 Planarity : 0.004 0.049 3192 Dihedral : 6.399 80.749 2677 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.39 % Favored : 93.52 % Rotamer: Outliers : 2.38 % Allowed : 14.64 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2270 helix: 1.90 (0.14), residues: 1393 sheet: -0.22 (0.56), residues: 76 loop : -1.14 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 372 HIS 0.007 0.001 HIS D 358 PHE 0.024 0.001 PHE B 720 TYR 0.014 0.001 TYR A 511 ARG 0.007 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 432 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8599 (mm-30) REVERT: A 419 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8229 (m-40) REVERT: A 471 ASP cc_start: 0.8236 (m-30) cc_final: 0.7754 (m-30) REVERT: A 511 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6940 (p90) REVERT: A 540 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8928 (p) REVERT: A 579 ARG cc_start: 0.8271 (mtm180) cc_final: 0.8052 (mtt-85) REVERT: A 700 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 721 ARG cc_start: 0.6630 (mmt180) cc_final: 0.6259 (mmt180) REVERT: D 223 ASN cc_start: 0.8201 (m110) cc_final: 0.7943 (m110) REVERT: D 363 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7706 (tpp80) REVERT: D 471 ASP cc_start: 0.8283 (m-30) cc_final: 0.7880 (t0) REVERT: D 504 LYS cc_start: 0.8511 (tttt) cc_final: 0.8106 (tppt) REVERT: D 698 LYS cc_start: 0.8854 (mttt) cc_final: 0.8541 (mmtt) REVERT: C 199 TYR cc_start: 0.6406 (m-80) cc_final: 0.5578 (m-10) REVERT: C 213 ASN cc_start: 0.8471 (t0) cc_final: 0.8096 (t0) REVERT: C 304 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7442 (p90) REVERT: C 363 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7414 (tpp-160) REVERT: C 472 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7423 (t80) REVERT: C 494 GLN cc_start: 0.8088 (mt0) cc_final: 0.7826 (tt0) REVERT: C 496 PHE cc_start: 0.8643 (t80) cc_final: 0.8237 (m-10) REVERT: C 504 LYS cc_start: 0.8515 (tptt) cc_final: 0.7988 (mmtt) REVERT: C 727 GLN cc_start: 0.6369 (tt0) cc_final: 0.5970 (tt0) REVERT: B 291 LEU cc_start: 0.9378 (mt) cc_final: 0.9066 (mt) REVERT: B 374 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6293 (t80) REVERT: B 460 LEU cc_start: 0.7825 (mt) cc_final: 0.7599 (pp) REVERT: B 472 TYR cc_start: 0.7749 (m-80) cc_final: 0.7316 (m-10) REVERT: B 496 PHE cc_start: 0.8539 (t80) cc_final: 0.8205 (m-10) outliers start: 48 outliers final: 37 residues processed: 460 average time/residue: 0.3022 time to fit residues: 209.6758 Evaluate side-chains 460 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 417 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 191 optimal weight: 0.0980 chunk 201 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS C 223 ASN C 410 HIS B 410 HIS ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19081 Z= 0.153 Angle : 0.562 14.957 25839 Z= 0.284 Chirality : 0.038 0.285 2914 Planarity : 0.003 0.049 3192 Dihedral : 6.323 88.944 2677 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 2.38 % Allowed : 15.29 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2270 helix: 1.88 (0.14), residues: 1391 sheet: -0.15 (0.56), residues: 76 loop : -1.16 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 372 HIS 0.004 0.001 HIS A 378 PHE 0.022 0.001 PHE C 266 TYR 0.016 0.001 TYR A 309 ARG 0.005 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 434 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.9217 (mm) cc_final: 0.8806 (tt) REVERT: A 311 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8606 (mm-30) REVERT: A 419 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8254 (m-40) REVERT: A 471 ASP cc_start: 0.8223 (m-30) cc_final: 0.7771 (m-30) REVERT: A 491 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: A 511 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6783 (p90) REVERT: A 540 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8903 (p) REVERT: A 575 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7295 (ptp-170) REVERT: A 579 ARG cc_start: 0.8251 (mtm180) cc_final: 0.8047 (mtt-85) REVERT: A 700 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 721 ARG cc_start: 0.6548 (mmt180) cc_final: 0.6122 (mmt180) REVERT: D 223 ASN cc_start: 0.8202 (m110) cc_final: 0.7933 (m110) REVERT: D 268 LEU cc_start: 0.8974 (mt) cc_final: 0.8752 (mt) REVERT: D 363 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7698 (tpp80) REVERT: D 471 ASP cc_start: 0.8201 (m-30) cc_final: 0.7793 (t0) REVERT: D 504 LYS cc_start: 0.8478 (tttt) cc_final: 0.8083 (tppt) REVERT: D 592 SER cc_start: 0.9400 (m) cc_final: 0.9185 (m) REVERT: D 698 LYS cc_start: 0.8841 (mttt) cc_final: 0.8523 (mmtt) REVERT: C 199 TYR cc_start: 0.6351 (m-80) cc_final: 0.5524 (m-10) REVERT: C 213 ASN cc_start: 0.8389 (t0) cc_final: 0.8039 (t0) REVERT: C 304 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7216 (p90) REVERT: C 363 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7353 (tpp-160) REVERT: C 472 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7428 (t80) REVERT: C 494 GLN cc_start: 0.8063 (mt0) cc_final: 0.7806 (tt0) REVERT: C 496 PHE cc_start: 0.8644 (t80) cc_final: 0.8265 (m-10) REVERT: C 504 LYS cc_start: 0.8496 (tptt) cc_final: 0.8005 (mmtt) REVERT: B 288 LEU cc_start: 0.8664 (mt) cc_final: 0.8437 (mt) REVERT: B 291 LEU cc_start: 0.9373 (mt) cc_final: 0.9065 (mt) REVERT: B 374 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6278 (t80) REVERT: B 472 TYR cc_start: 0.7735 (m-80) cc_final: 0.7305 (m-10) REVERT: B 491 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7404 (mmm-85) REVERT: B 496 PHE cc_start: 0.8517 (t80) cc_final: 0.8210 (m-10) REVERT: B 677 MET cc_start: 0.8856 (ttm) cc_final: 0.8648 (ttt) outliers start: 48 outliers final: 35 residues processed: 462 average time/residue: 0.3019 time to fit residues: 211.4744 Evaluate side-chains 463 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 421 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS D 393 ASN C 223 ASN C 301 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19081 Z= 0.236 Angle : 0.607 18.153 25839 Z= 0.302 Chirality : 0.040 0.296 2914 Planarity : 0.004 0.049 3192 Dihedral : 6.373 86.196 2677 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.61 % Rotamer: Outliers : 2.48 % Allowed : 15.29 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2270 helix: 1.85 (0.14), residues: 1392 sheet: -0.26 (0.56), residues: 76 loop : -1.19 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 372 HIS 0.004 0.001 HIS A 378 PHE 0.023 0.001 PHE C 266 TYR 0.016 0.001 TYR A 309 ARG 0.008 0.000 ARG B 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 423 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8607 (mm-30) REVERT: A 419 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: A 471 ASP cc_start: 0.8243 (m-30) cc_final: 0.7785 (m-30) REVERT: A 511 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6884 (p90) REVERT: A 540 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 700 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 721 ARG cc_start: 0.6713 (mmt180) cc_final: 0.6278 (mmt180) REVERT: D 223 ASN cc_start: 0.8233 (m110) cc_final: 0.7963 (m110) REVERT: D 363 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7720 (tpp80) REVERT: D 504 LYS cc_start: 0.8497 (tttt) cc_final: 0.8090 (tppt) REVERT: D 698 LYS cc_start: 0.8851 (mttt) cc_final: 0.8531 (mmtt) REVERT: C 199 TYR cc_start: 0.6358 (m-80) cc_final: 0.5541 (m-10) REVERT: C 213 ASN cc_start: 0.8432 (t0) cc_final: 0.8082 (t0) REVERT: C 246 TYR cc_start: 0.8485 (t80) cc_final: 0.8136 (t80) REVERT: C 276 ASP cc_start: 0.8269 (t0) cc_final: 0.7903 (t0) REVERT: C 304 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7323 (p90) REVERT: C 363 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7298 (tpp-160) REVERT: C 472 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7436 (t80) REVERT: C 494 GLN cc_start: 0.8101 (mt0) cc_final: 0.7852 (tt0) REVERT: C 496 PHE cc_start: 0.8671 (t80) cc_final: 0.8259 (m-10) REVERT: C 504 LYS cc_start: 0.8575 (tptt) cc_final: 0.8085 (mmtt) REVERT: B 288 LEU cc_start: 0.8719 (mt) cc_final: 0.8494 (mt) REVERT: B 291 LEU cc_start: 0.9381 (mt) cc_final: 0.9066 (mt) REVERT: B 472 TYR cc_start: 0.7776 (m-80) cc_final: 0.7332 (m-10) REVERT: B 496 PHE cc_start: 0.8523 (t80) cc_final: 0.8195 (m-10) outliers start: 50 outliers final: 36 residues processed: 452 average time/residue: 0.3020 time to fit residues: 205.7536 Evaluate side-chains 456 residues out of total 2015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 415 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN D 206 HIS C 223 ASN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097305 restraints weight = 30383.843| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.63 r_work: 0.2972 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19081 Z= 0.155 Angle : 0.587 16.117 25839 Z= 0.292 Chirality : 0.038 0.276 2914 Planarity : 0.004 0.049 3192 Dihedral : 6.194 81.189 2677 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.99 % Allowed : 15.93 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2270 helix: 1.93 (0.14), residues: 1375 sheet: -0.23 (0.57), residues: 76 loop : -1.11 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 372 HIS 0.005 0.000 HIS C 358 PHE 0.018 0.001 PHE B 720 TYR 0.015 0.001 TYR A 309 ARG 0.009 0.000 ARG B 743 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4926.20 seconds wall clock time: 88 minutes 54.37 seconds (5334.37 seconds total)