Starting phenix.real_space_refine on Sat Feb 17 09:27:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mza_24087/02_2024/7mza_24087_updated.pdb" } resolution = 3.46 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 2 5.49 5 S 104 5.16 5 Na 1 4.78 5 C 11943 2.51 5 N 2931 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18242 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4667 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 562} 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: "B" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4676 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 563} Chain: "C" 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: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 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} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.47, per 1000 atoms: 0.52 Number of scatterers: 18242 At special positions: 0 Unit cell: (124.266, 123.432, 118.428, 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 104 16.00 P 2 15.00 Na 1 11.00 O 3261 8.00 N 2931 7.00 C 11943 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=2.05 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: 7.45 Conformation dependent library (CDL) restraints added in 3.2 seconds 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 4 sheets defined 58.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 171 through 183 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' 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 258 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 removed outlier: 3.539A pdb=" N PHE A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) 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: 3.948A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.306A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.232A 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: 3.918A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.758A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.067A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.112A 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 686 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 removed outlier: 3.588A pdb=" N PHE D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) 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 342 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.761A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) 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 409 through 414 removed outlier: 4.498A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 5.018A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.215A 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: 4.025A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.713A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.959A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.005A 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 Processing helix chain 'D' and resid 690 through 711 removed outlier: 3.822A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) 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 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: 3.940A 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: 5.219A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.346A 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: 4.072A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.975A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.064A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 673 through 686 Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.669A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.637A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) 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: 4.958A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.310A 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: 4.107A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.716A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.922A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 673 through 688 Processing helix chain 'C' and resid 690 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.987A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.561A 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: 3.954A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.924A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 4.048A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2481 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: 5.56 Time building geometry restraints manager: 7.85 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: 2827 1.30 - 1.43: 5209 1.43 - 1.56: 10462 1.56 - 1.69: 13 1.69 - 1.82: 170 Bond restraints: 18681 Sorted by residual: bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.183 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.190 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" CAV 6EU C 901 " pdb=" CBB 6EU C 901 " ideal model delta sigma weight residual 1.330 1.522 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.520 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" CAL 6EU D 901 " pdb=" OAB 6EU D 901 " ideal model delta sigma weight residual 1.415 1.245 0.170 2.00e-02 2.50e+03 7.18e+01 ... (remaining 18676 not shown) Histogram of bond angle deviations from ideal: 96.27 - 103.84: 199 103.84 - 111.40: 8238 111.40 - 118.97: 6740 118.97 - 126.54: 9921 126.54 - 134.10: 218 Bond angle restraints: 25316 Sorted by residual: angle pdb=" N SER D 722 " pdb=" CA SER D 722 " pdb=" CB SER D 722 " ideal model delta sigma weight residual 114.17 107.98 6.19 1.14e+00 7.69e-01 2.95e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 130.29 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 130.06 -14.68 3.00e+00 1.11e-01 2.39e+01 angle pdb=" N SER C 722 " pdb=" CA SER C 722 " pdb=" CB SER C 722 " ideal model delta sigma weight residual 114.17 108.91 5.26 1.14e+00 7.69e-01 2.13e+01 ... (remaining 25311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 10756 21.68 - 43.35: 298 43.35 - 65.03: 60 65.03 - 86.70: 19 86.70 - 108.38: 4 Dihedral angle restraints: 11137 sinusoidal: 4570 harmonic: 6567 Sorted by residual: dihedral pdb=" CA TYR D 653 " pdb=" C TYR D 653 " pdb=" N ASP D 654 " pdb=" CA ASP D 654 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLY D 558 " pdb=" C GLY D 558 " pdb=" N PHE D 559 " pdb=" CA PHE D 559 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG D 721 " pdb=" C ARG D 721 " pdb=" N SER D 722 " pdb=" CA SER D 722 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 11134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.012: 2853 1.012 - 2.023: 0 2.023 - 3.035: 0 3.035 - 4.047: 0 4.047 - 5.059: 4 Chirality restraints: 2857 Sorted by residual: chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.56 -5.06 2.00e-01 2.50e+01 6.40e+02 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 2.54 -5.05 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C XJ7 A 801 " pdb=" O XJ7 A 801 " pdb=" C1 XJ7 A 801 " pdb=" C25 XJ7 A 801 " both_signs ideal model delta sigma weight residual False 2.51 -2.50 5.01 2.00e-01 2.50e+01 6.27e+02 ... (remaining 2854 not shown) Planarity restraints: 3120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " 0.099 2.00e-02 2.50e+03 1.73e-01 3.01e+02 pdb=" CAV 6EU D 901 " -0.300 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " 0.101 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " 0.095 2.00e-02 2.50e+03 1.67e-01 2.78e+02 pdb=" CAV 6EU C 901 " -0.289 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " 0.095 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " 0.099 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 2.80e-02 7.82e+00 pdb=" C GLY B 548 " -0.048 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 ... (remaining 3117 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 140 2.56 - 3.14: 15849 3.14 - 3.73: 28410 3.73 - 4.31: 40029 4.31 - 4.90: 66687 Nonbonded interactions: 151115 Sorted by model distance: nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 1.974 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 1.975 2.440 nonbonded pdb=" O ILE C 689 " pdb=" OG SER C 693 " model vdw 2.065 2.440 nonbonded pdb=" OE2 GLU A 570 " pdb=" O11 XJ7 A 801 " model vdw 2.092 2.440 nonbonded pdb=" OE2 GLU A 416 " pdb=" NE ARG A 420 " model vdw 2.207 2.520 ... (remaining 151110 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.970 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 48.970 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 0.239 18681 Z= 0.624 Angle : 0.829 14.911 25316 Z= 0.440 Chirality : 0.194 5.059 2857 Planarity : 0.006 0.173 3120 Dihedral : 11.893 108.379 6916 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.66 % Allowed : 1.88 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2221 helix: 1.50 (0.13), residues: 1372 sheet: -1.69 (0.50), residues: 76 loop : -1.15 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 697 HIS 0.005 0.001 HIS D 206 PHE 0.024 0.002 PHE D 649 TYR 0.032 0.002 TYR D 511 ARG 0.004 0.001 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 855 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: symmetry clash revert: symmetry clash REVERT: A 288 LEU cc_start: 0.9329 (mt) cc_final: 0.9073 (mt) REVERT: A 372 TRP cc_start: 0.8247 (p-90) cc_final: 0.7772 (p-90) REVERT: A 378 HIS cc_start: 0.8225 (p-80) cc_final: 0.7976 (p-80) REVERT: A 416 GLU cc_start: 0.7073 (tp30) cc_final: 0.6578 (tp30) REVERT: A 438 PHE cc_start: 0.9401 (t80) cc_final: 0.9122 (t80) REVERT: A 478 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 491 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.7382 (ttt180) REVERT: A 568 MET cc_start: 0.9003 (mtm) cc_final: 0.8800 (mtt) REVERT: A 572 MET cc_start: 0.9169 (mmp) cc_final: 0.8887 (mmt) REVERT: A 660 ILE cc_start: 0.9532 (tp) cc_final: 0.9303 (tp) REVERT: A 698 LYS cc_start: 0.9049 (mttt) cc_final: 0.8793 (mtmm) REVERT: D 357 ILE cc_start: 0.8799 (mt) cc_final: 0.8237 (mt) REVERT: D 363 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7674 (mmm-85) REVERT: D 378 HIS cc_start: 0.7790 (p90) cc_final: 0.7111 (p-80) REVERT: D 420 ARG cc_start: 0.8733 (mmt180) cc_final: 0.8521 (mmm-85) REVERT: D 423 GLN cc_start: 0.8634 (tp40) cc_final: 0.8372 (tp40) REVERT: D 425 LYS cc_start: 0.9038 (mttm) cc_final: 0.8760 (mttt) REVERT: D 427 ASP cc_start: 0.9151 (m-30) cc_final: 0.8945 (m-30) REVERT: D 438 PHE cc_start: 0.9323 (t80) cc_final: 0.9100 (t80) REVERT: D 449 THR cc_start: 0.9612 (m) cc_final: 0.9369 (p) REVERT: D 481 SER cc_start: 0.9159 (m) cc_final: 0.8930 (p) REVERT: D 483 SER cc_start: 0.9440 (t) cc_final: 0.8958 (p) REVERT: D 551 ASN cc_start: 0.9324 (m-40) cc_final: 0.9067 (m110) REVERT: D 628 ASN cc_start: 0.8774 (t0) cc_final: 0.8238 (t0) REVERT: D 630 LEU cc_start: 0.9401 (tp) cc_final: 0.9173 (tp) REVERT: D 636 GLU cc_start: 0.8944 (tp30) cc_final: 0.8422 (tp30) REVERT: D 689 ILE cc_start: 0.8852 (pt) cc_final: 0.6739 (pt) REVERT: B 210 GLU cc_start: 0.8867 (pt0) cc_final: 0.8513 (pt0) REVERT: B 310 ASN cc_start: 0.9366 (t0) cc_final: 0.9093 (t0) REVERT: B 343 SER cc_start: 0.9073 (m) cc_final: 0.8871 (m) REVERT: B 368 LYS cc_start: 0.9248 (tttt) cc_final: 0.9014 (tttm) REVERT: B 421 LEU cc_start: 0.9569 (tp) cc_final: 0.9344 (tt) REVERT: B 431 LYS cc_start: 0.8984 (tttt) cc_final: 0.8704 (ttpp) REVERT: B 432 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7121 (mmm160) REVERT: B 472 TYR cc_start: 0.7969 (m-80) cc_final: 0.7606 (m-80) REVERT: B 526 SER cc_start: 0.9575 (t) cc_final: 0.9230 (m) REVERT: B 725 LEU cc_start: 0.8976 (mt) cc_final: 0.8620 (mp) REVERT: C 211 ARG cc_start: 0.8709 (mmt-90) cc_final: 0.8485 (mmm-85) REVERT: C 213 ASN cc_start: 0.9133 (t0) cc_final: 0.8796 (t0) REVERT: C 267 LEU cc_start: 0.9547 (mt) cc_final: 0.9336 (mt) REVERT: C 273 GLN cc_start: 0.8098 (tp40) cc_final: 0.7816 (tp-100) REVERT: C 309 TYR cc_start: 0.9360 (t80) cc_final: 0.8745 (t80) REVERT: C 326 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 374 TYR cc_start: 0.8399 (t80) cc_final: 0.8170 (t80) REVERT: C 414 LEU cc_start: 0.9100 (mt) cc_final: 0.8835 (mp) REVERT: C 494 GLN cc_start: 0.8869 (mt0) cc_final: 0.8657 (mt0) REVERT: C 551 ASN cc_start: 0.9368 (m-40) cc_final: 0.9084 (m-40) REVERT: C 561 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: C 632 SER cc_start: 0.9465 (m) cc_final: 0.9252 (p) REVERT: C 636 GLU cc_start: 0.8681 (tp30) cc_final: 0.8153 (tp30) REVERT: C 648 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8178 (tp30) outliers start: 13 outliers final: 3 residues processed: 863 average time/residue: 0.3289 time to fit residues: 410.5203 Evaluate side-chains 571 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 566 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 648 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 172 optimal weight: 0.0070 chunk 66 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 310 ASN A 393 ASN A 676 ASN D 393 ASN D 494 GLN B 393 ASN B 561 GLN B 676 ASN C 419 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18681 Z= 0.169 Angle : 0.595 10.462 25316 Z= 0.308 Chirality : 0.040 0.314 2857 Planarity : 0.004 0.048 3120 Dihedral : 7.983 87.802 2698 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Rotamer: Outliers : 2.34 % Allowed : 12.44 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2221 helix: 1.68 (0.14), residues: 1381 sheet: -1.20 (0.54), residues: 76 loop : -1.09 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.006 0.001 HIS D 410 PHE 0.021 0.002 PHE C 507 TYR 0.026 0.001 TYR D 511 ARG 0.005 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 646 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 420 ARG cc_start: 0.8814 (ttm110) cc_final: 0.7960 (tpp80) REVERT: A 438 PHE cc_start: 0.9299 (t80) cc_final: 0.8982 (t80) REVERT: A 478 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 499 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8161 (mmm-85) REVERT: A 560 GLN cc_start: 0.8740 (tp40) cc_final: 0.8460 (tp40) REVERT: A 568 MET cc_start: 0.8933 (mtm) cc_final: 0.8677 (mtt) REVERT: A 572 MET cc_start: 0.9093 (mmp) cc_final: 0.8721 (mmt) REVERT: A 660 ILE cc_start: 0.9519 (tp) cc_final: 0.9220 (tp) REVERT: A 698 LYS cc_start: 0.8992 (mttt) cc_final: 0.8759 (mtmm) REVERT: A 704 THR cc_start: 0.9501 (m) cc_final: 0.9276 (p) REVERT: A 745 ASP cc_start: 0.8083 (m-30) cc_final: 0.7820 (t0) REVERT: D 374 TYR cc_start: 0.8037 (t80) cc_final: 0.7578 (m-80) REVERT: D 408 ASN cc_start: 0.8452 (m-40) cc_final: 0.8204 (m110) REVERT: D 420 ARG cc_start: 0.8702 (mmt180) cc_final: 0.8488 (mmm-85) REVERT: D 423 GLN cc_start: 0.8665 (tp40) cc_final: 0.8303 (tp40) REVERT: D 425 LYS cc_start: 0.8896 (mttm) cc_final: 0.8599 (mttt) REVERT: D 427 ASP cc_start: 0.9039 (m-30) cc_final: 0.8825 (m-30) REVERT: D 481 SER cc_start: 0.9150 (m) cc_final: 0.8931 (p) REVERT: D 483 SER cc_start: 0.9362 (t) cc_final: 0.8990 (p) REVERT: D 628 ASN cc_start: 0.8682 (t0) cc_final: 0.8167 (t0) REVERT: D 636 GLU cc_start: 0.8708 (tp30) cc_final: 0.8470 (tp30) REVERT: D 698 LYS cc_start: 0.8941 (mttp) cc_final: 0.8618 (mttt) REVERT: B 210 GLU cc_start: 0.8798 (pt0) cc_final: 0.8311 (pt0) REVERT: B 310 ASN cc_start: 0.9250 (t0) cc_final: 0.8998 (t0) REVERT: B 353 LEU cc_start: 0.9593 (mt) cc_final: 0.9379 (mt) REVERT: B 363 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7823 (mmt90) REVERT: B 392 LYS cc_start: 0.8950 (ptpt) cc_final: 0.8743 (ptpt) REVERT: B 432 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7042 (mmm160) REVERT: B 472 TYR cc_start: 0.8065 (m-80) cc_final: 0.7674 (m-80) REVERT: B 478 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 644 MET cc_start: 0.8295 (mmp) cc_final: 0.8048 (mmp) REVERT: B 684 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 746 GLU cc_start: 0.8140 (tp30) cc_final: 0.7914 (tp30) REVERT: C 206 HIS cc_start: 0.9063 (m90) cc_final: 0.8733 (m90) REVERT: C 273 GLN cc_start: 0.8037 (tp40) cc_final: 0.7680 (tp-100) REVERT: C 309 TYR cc_start: 0.9312 (t80) cc_final: 0.8742 (t80) REVERT: C 326 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7078 (mt-10) REVERT: C 339 LEU cc_start: 0.9201 (tp) cc_final: 0.8948 (tt) REVERT: C 372 TRP cc_start: 0.8529 (p-90) cc_final: 0.8135 (p-90) REVERT: C 374 TYR cc_start: 0.8291 (t80) cc_final: 0.8088 (t80) REVERT: C 414 LEU cc_start: 0.8929 (mt) cc_final: 0.8675 (mp) REVERT: C 428 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8619 (ttm-80) REVERT: C 494 GLN cc_start: 0.8959 (mt0) cc_final: 0.8576 (mt0) REVERT: C 551 ASN cc_start: 0.9253 (m-40) cc_final: 0.8980 (m-40) REVERT: C 561 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: C 632 SER cc_start: 0.9437 (m) cc_final: 0.9228 (p) REVERT: C 689 ILE cc_start: 0.8843 (pt) cc_final: 0.8487 (pt) REVERT: C 724 LYS cc_start: 0.8360 (tppt) cc_final: 0.8122 (tppp) outliers start: 46 outliers final: 29 residues processed: 668 average time/residue: 0.2897 time to fit residues: 293.0980 Evaluate side-chains 604 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 574 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 198 optimal weight: 0.0030 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN D 676 ASN B 358 HIS B 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18681 Z= 0.221 Angle : 0.575 10.666 25316 Z= 0.298 Chirality : 0.039 0.197 2857 Planarity : 0.004 0.049 3120 Dihedral : 7.296 76.077 2694 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.63 % Favored : 94.15 % Rotamer: Outliers : 3.10 % Allowed : 15.29 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2221 helix: 1.62 (0.14), residues: 1395 sheet: -1.02 (0.55), residues: 76 loop : -1.29 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 372 HIS 0.004 0.001 HIS D 410 PHE 0.020 0.001 PHE A 369 TYR 0.034 0.001 TYR D 511 ARG 0.005 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 583 time to evaluate : 2.099 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 214 MET cc_start: 0.8477 (pmm) cc_final: 0.8153 (pmm) REVERT: A 372 TRP cc_start: 0.7916 (p-90) cc_final: 0.7673 (p-90) REVERT: A 416 GLU cc_start: 0.6597 (tp30) cc_final: 0.6029 (tp30) REVERT: A 420 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8289 (tpp80) REVERT: A 438 PHE cc_start: 0.9344 (t80) cc_final: 0.9051 (t80) REVERT: A 478 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7969 (mt-10) REVERT: A 560 GLN cc_start: 0.8768 (tp40) cc_final: 0.8483 (tp40) REVERT: A 572 MET cc_start: 0.9086 (mmp) cc_final: 0.8818 (mmt) REVERT: A 648 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 660 ILE cc_start: 0.9528 (tp) cc_final: 0.9208 (tp) REVERT: A 698 LYS cc_start: 0.9004 (mttt) cc_final: 0.8763 (mtmm) REVERT: A 745 ASP cc_start: 0.8014 (m-30) cc_final: 0.7805 (t0) REVERT: D 374 TYR cc_start: 0.8164 (t80) cc_final: 0.7695 (m-80) REVERT: D 420 ARG cc_start: 0.8692 (mmt180) cc_final: 0.8467 (mmm-85) REVERT: D 423 GLN cc_start: 0.8674 (tp40) cc_final: 0.8310 (tp40) REVERT: D 425 LYS cc_start: 0.8889 (mttm) cc_final: 0.8586 (mttt) REVERT: D 427 ASP cc_start: 0.9042 (m-30) cc_final: 0.8832 (m-30) REVERT: D 429 PHE cc_start: 0.7867 (t80) cc_final: 0.7616 (t80) REVERT: D 481 SER cc_start: 0.9159 (m) cc_final: 0.8921 (p) REVERT: D 483 SER cc_start: 0.9382 (t) cc_final: 0.9004 (p) REVERT: D 562 MET cc_start: 0.8646 (mmm) cc_final: 0.8284 (mtt) REVERT: D 628 ASN cc_start: 0.8668 (t0) cc_final: 0.8143 (t0) REVERT: D 636 GLU cc_start: 0.8810 (tp30) cc_final: 0.8601 (tp30) REVERT: D 656 LYS cc_start: 0.9300 (tttt) cc_final: 0.9042 (ttpt) REVERT: D 698 LYS cc_start: 0.9018 (mttp) cc_final: 0.8711 (mttt) REVERT: D 743 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7276 (mtp180) REVERT: B 310 ASN cc_start: 0.9247 (t0) cc_final: 0.9014 (t0) REVERT: B 432 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7032 (mmm160) REVERT: B 472 TYR cc_start: 0.8153 (m-80) cc_final: 0.7672 (m-80) REVERT: B 478 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 644 MET cc_start: 0.8352 (mmp) cc_final: 0.8082 (mmp) REVERT: B 684 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 746 GLU cc_start: 0.8119 (tp30) cc_final: 0.7846 (tp30) REVERT: C 206 HIS cc_start: 0.9085 (m90) cc_final: 0.8756 (m90) REVERT: C 309 TYR cc_start: 0.9401 (t80) cc_final: 0.8884 (t80) REVERT: C 326 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 372 TRP cc_start: 0.8678 (p-90) cc_final: 0.8021 (p-90) REVERT: C 414 LEU cc_start: 0.8962 (mt) cc_final: 0.8696 (mp) REVERT: C 428 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8634 (ttm-80) REVERT: C 494 GLN cc_start: 0.8940 (mt0) cc_final: 0.8528 (mt0) REVERT: C 551 ASN cc_start: 0.9252 (m-40) cc_final: 0.8957 (m-40) REVERT: C 572 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8677 (mmp) REVERT: C 632 SER cc_start: 0.9459 (m) cc_final: 0.9255 (p) REVERT: C 724 LYS cc_start: 0.8362 (tppt) cc_final: 0.8086 (tppp) outliers start: 61 outliers final: 44 residues processed: 607 average time/residue: 0.2876 time to fit residues: 265.8289 Evaluate side-chains 595 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 550 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 GLN D 676 ASN B 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18681 Z= 0.176 Angle : 0.554 9.715 25316 Z= 0.287 Chirality : 0.038 0.167 2857 Planarity : 0.004 0.049 3120 Dihedral : 6.757 72.294 2691 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 2.89 % Allowed : 16.76 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2221 helix: 1.63 (0.14), residues: 1389 sheet: -0.90 (0.56), residues: 76 loop : -1.32 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 372 HIS 0.004 0.001 HIS D 410 PHE 0.022 0.001 PHE D 369 TYR 0.035 0.001 TYR D 511 ARG 0.004 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 589 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8537 (pmm) cc_final: 0.8270 (pmm) REVERT: A 438 PHE cc_start: 0.9364 (t80) cc_final: 0.9075 (t80) REVERT: A 478 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 648 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 660 ILE cc_start: 0.9531 (tp) cc_final: 0.9200 (tp) REVERT: A 698 LYS cc_start: 0.8993 (mttt) cc_final: 0.8748 (mtmm) REVERT: A 717 ARG cc_start: 0.7208 (mmp-170) cc_final: 0.6583 (mmp80) REVERT: A 745 ASP cc_start: 0.8011 (m-30) cc_final: 0.7758 (t0) REVERT: D 423 GLN cc_start: 0.8619 (tp40) cc_final: 0.8281 (tp40) REVERT: D 425 LYS cc_start: 0.8856 (mttm) cc_final: 0.8583 (mttt) REVERT: D 481 SER cc_start: 0.9162 (m) cc_final: 0.8929 (p) REVERT: D 483 SER cc_start: 0.9378 (t) cc_final: 0.8998 (p) REVERT: D 496 PHE cc_start: 0.8295 (t80) cc_final: 0.7773 (m-10) REVERT: D 526 SER cc_start: 0.9387 (t) cc_final: 0.9086 (p) REVERT: D 628 ASN cc_start: 0.8622 (t0) cc_final: 0.8145 (t0) REVERT: D 656 LYS cc_start: 0.9292 (tttt) cc_final: 0.9044 (ttpt) REVERT: D 709 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6990 (mt-10) REVERT: D 743 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7342 (mtp180) REVERT: B 310 ASN cc_start: 0.9231 (t0) cc_final: 0.9005 (t0) REVERT: B 432 ARG cc_start: 0.7857 (mtt90) cc_final: 0.6968 (mmm160) REVERT: B 472 TYR cc_start: 0.8147 (m-80) cc_final: 0.7648 (m-80) REVERT: B 478 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 707 ASP cc_start: 0.8704 (t0) cc_final: 0.8502 (t0) REVERT: B 746 GLU cc_start: 0.8125 (tp30) cc_final: 0.7886 (tp30) REVERT: C 206 HIS cc_start: 0.9074 (m90) cc_final: 0.8684 (m90) REVERT: C 309 TYR cc_start: 0.9429 (t80) cc_final: 0.8856 (t80) REVERT: C 326 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 372 TRP cc_start: 0.8673 (p-90) cc_final: 0.8101 (p-90) REVERT: C 414 LEU cc_start: 0.8952 (mt) cc_final: 0.8686 (mp) REVERT: C 428 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8630 (ttm-80) REVERT: C 438 PHE cc_start: 0.9324 (t80) cc_final: 0.8995 (t80) REVERT: C 491 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8144 (tpp80) REVERT: C 572 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8649 (mmp) outliers start: 57 outliers final: 45 residues processed: 615 average time/residue: 0.2763 time to fit residues: 261.0966 Evaluate side-chains 606 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 559 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 GLN B 301 ASN B 676 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18681 Z= 0.213 Angle : 0.559 9.382 25316 Z= 0.290 Chirality : 0.039 0.234 2857 Planarity : 0.004 0.049 3120 Dihedral : 6.448 74.637 2691 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.06 % Rotamer: Outliers : 3.30 % Allowed : 17.83 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2221 helix: 1.58 (0.14), residues: 1391 sheet: -0.82 (0.56), residues: 76 loop : -1.33 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 372 HIS 0.003 0.001 HIS D 410 PHE 0.025 0.001 PHE A 266 TYR 0.029 0.001 TYR D 511 ARG 0.004 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 581 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LEU cc_start: 0.9406 (mt) cc_final: 0.9115 (mt) REVERT: A 420 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8467 (tpp80) REVERT: A 438 PHE cc_start: 0.9375 (t80) cc_final: 0.9073 (t80) REVERT: A 478 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 498 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 648 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 660 ILE cc_start: 0.9547 (tp) cc_final: 0.9177 (tp) REVERT: A 698 LYS cc_start: 0.9020 (mttt) cc_final: 0.8767 (mtmm) REVERT: D 425 LYS cc_start: 0.8836 (mttm) cc_final: 0.8544 (mttt) REVERT: D 431 LYS cc_start: 0.8370 (tttt) cc_final: 0.8074 (mttt) REVERT: D 481 SER cc_start: 0.9174 (m) cc_final: 0.8902 (p) REVERT: D 483 SER cc_start: 0.9387 (t) cc_final: 0.9003 (p) REVERT: D 496 PHE cc_start: 0.8272 (t80) cc_final: 0.7729 (m-10) REVERT: D 526 SER cc_start: 0.9424 (t) cc_final: 0.9119 (p) REVERT: D 628 ASN cc_start: 0.8589 (t0) cc_final: 0.8120 (t0) REVERT: D 656 LYS cc_start: 0.9296 (tttt) cc_final: 0.9045 (ttpt) REVERT: D 709 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7066 (mt-10) REVERT: D 743 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7563 (mtp180) REVERT: B 310 ASN cc_start: 0.9228 (t0) cc_final: 0.9009 (t0) REVERT: B 472 TYR cc_start: 0.8173 (m-80) cc_final: 0.7664 (m-80) REVERT: B 478 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 206 HIS cc_start: 0.8905 (m90) cc_final: 0.8518 (m90) REVERT: C 288 LEU cc_start: 0.9429 (mt) cc_final: 0.9182 (mt) REVERT: C 308 MET cc_start: 0.9106 (tpp) cc_final: 0.8723 (ttm) REVERT: C 309 TYR cc_start: 0.9467 (t80) cc_final: 0.9075 (t80) REVERT: C 326 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7523 (mt-10) REVERT: C 372 TRP cc_start: 0.8758 (p-90) cc_final: 0.8126 (p-90) REVERT: C 414 LEU cc_start: 0.8931 (mt) cc_final: 0.8620 (mp) REVERT: C 447 ILE cc_start: 0.9337 (mt) cc_final: 0.9131 (mt) REVERT: C 494 GLN cc_start: 0.8808 (mt0) cc_final: 0.8554 (mt0) outliers start: 65 outliers final: 51 residues processed: 611 average time/residue: 0.2844 time to fit residues: 265.6941 Evaluate side-chains 597 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 546 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 676 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18681 Z= 0.152 Angle : 0.546 8.932 25316 Z= 0.282 Chirality : 0.038 0.211 2857 Planarity : 0.003 0.048 3120 Dihedral : 6.145 74.874 2691 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.29 % Allowed : 19.55 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2221 helix: 1.63 (0.14), residues: 1379 sheet: -0.78 (0.57), residues: 76 loop : -1.29 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 372 HIS 0.004 0.001 HIS D 410 PHE 0.040 0.001 PHE C 489 TYR 0.038 0.001 TYR B 309 ARG 0.005 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 603 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 260 GLN cc_start: 0.8525 (mt0) cc_final: 0.8050 (mt0) REVERT: A 420 ARG cc_start: 0.8854 (tpp80) cc_final: 0.8349 (tpp80) REVERT: A 438 PHE cc_start: 0.9367 (t80) cc_final: 0.9067 (t80) REVERT: A 478 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 572 MET cc_start: 0.8887 (mmp) cc_final: 0.8673 (mmm) REVERT: A 648 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 660 ILE cc_start: 0.9534 (tp) cc_final: 0.9159 (tp) REVERT: A 698 LYS cc_start: 0.9012 (mttt) cc_final: 0.8759 (mtmm) REVERT: A 717 ARG cc_start: 0.7231 (mmp-170) cc_final: 0.6589 (mmp80) REVERT: D 431 LYS cc_start: 0.8405 (tttt) cc_final: 0.8085 (mttt) REVERT: D 481 SER cc_start: 0.9147 (m) cc_final: 0.8877 (p) REVERT: D 483 SER cc_start: 0.9393 (t) cc_final: 0.9006 (p) REVERT: D 496 PHE cc_start: 0.8251 (t80) cc_final: 0.7757 (m-10) REVERT: D 526 SER cc_start: 0.9368 (t) cc_final: 0.9051 (p) REVERT: D 562 MET cc_start: 0.8361 (mmm) cc_final: 0.7962 (mtt) REVERT: D 628 ASN cc_start: 0.8547 (t0) cc_final: 0.8069 (t0) REVERT: D 656 LYS cc_start: 0.9273 (tttt) cc_final: 0.8994 (ttpt) REVERT: D 709 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7143 (mt-10) REVERT: D 743 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7688 (mtp180) REVERT: B 212 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7208 (mtt-85) REVERT: B 310 ASN cc_start: 0.9195 (t0) cc_final: 0.8984 (t0) REVERT: B 392 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8486 (mtmm) REVERT: B 472 TYR cc_start: 0.8150 (m-80) cc_final: 0.7637 (m-80) REVERT: B 478 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 206 HIS cc_start: 0.8939 (m90) cc_final: 0.8515 (m90) REVERT: C 288 LEU cc_start: 0.9420 (mt) cc_final: 0.9166 (mt) REVERT: C 305 VAL cc_start: 0.9623 (OUTLIER) cc_final: 0.9330 (m) REVERT: C 309 TYR cc_start: 0.9470 (t80) cc_final: 0.9081 (t80) REVERT: C 326 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 414 LEU cc_start: 0.8875 (mt) cc_final: 0.8555 (mp) REVERT: C 427 ASP cc_start: 0.8604 (m-30) cc_final: 0.8259 (m-30) REVERT: C 447 ILE cc_start: 0.9319 (mt) cc_final: 0.9106 (mt) REVERT: C 710 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8623 (tmtt) outliers start: 45 outliers final: 36 residues processed: 629 average time/residue: 0.2731 time to fit residues: 264.9509 Evaluate side-chains 617 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 580 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 410 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18681 Z= 0.334 Angle : 0.627 9.094 25316 Z= 0.322 Chirality : 0.041 0.368 2857 Planarity : 0.004 0.050 3120 Dihedral : 6.226 81.026 2691 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 3.30 % Allowed : 19.50 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2221 helix: 1.54 (0.14), residues: 1384 sheet: -0.94 (0.57), residues: 76 loop : -1.30 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 372 HIS 0.005 0.001 HIS B 289 PHE 0.030 0.002 PHE C 489 TYR 0.039 0.002 TYR B 309 ARG 0.007 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 559 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 420 ARG cc_start: 0.8885 (tpp80) cc_final: 0.8370 (tpp80) REVERT: A 438 PHE cc_start: 0.9408 (t80) cc_final: 0.9094 (t80) REVERT: A 478 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8015 (mt-10) REVERT: A 648 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 660 ILE cc_start: 0.9557 (tp) cc_final: 0.9196 (tp) REVERT: A 698 LYS cc_start: 0.9037 (mttt) cc_final: 0.8788 (mtmm) REVERT: D 431 LYS cc_start: 0.8423 (tttt) cc_final: 0.8101 (mttt) REVERT: D 449 THR cc_start: 0.9542 (m) cc_final: 0.9333 (p) REVERT: D 481 SER cc_start: 0.9130 (m) cc_final: 0.8919 (p) REVERT: D 483 SER cc_start: 0.9405 (t) cc_final: 0.9019 (p) REVERT: D 496 PHE cc_start: 0.8285 (t80) cc_final: 0.7732 (m-10) REVERT: D 526 SER cc_start: 0.9433 (t) cc_final: 0.9065 (p) REVERT: D 547 MET cc_start: 0.8446 (mmm) cc_final: 0.8174 (mmm) REVERT: D 628 ASN cc_start: 0.8657 (t0) cc_final: 0.8175 (t0) REVERT: D 656 LYS cc_start: 0.9315 (tttt) cc_final: 0.9037 (ttpt) REVERT: B 310 ASN cc_start: 0.9242 (t0) cc_final: 0.9040 (t0) REVERT: B 386 CYS cc_start: 0.9133 (m) cc_final: 0.8927 (m) REVERT: B 472 TYR cc_start: 0.8194 (m-80) cc_final: 0.7675 (m-80) REVERT: B 478 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 721 ARG cc_start: 0.7371 (mmt180) cc_final: 0.7003 (mmt180) REVERT: C 206 HIS cc_start: 0.8948 (m90) cc_final: 0.8554 (m90) REVERT: C 288 LEU cc_start: 0.9456 (mt) cc_final: 0.9209 (mt) REVERT: C 309 TYR cc_start: 0.9480 (t80) cc_final: 0.9069 (t80) REVERT: C 326 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7526 (mt-10) REVERT: C 372 TRP cc_start: 0.8780 (p-90) cc_final: 0.8224 (p-90) REVERT: C 427 ASP cc_start: 0.8606 (m-30) cc_final: 0.8296 (m-30) REVERT: C 447 ILE cc_start: 0.9343 (mt) cc_final: 0.9141 (mt) REVERT: C 710 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8657 (tmtt) outliers start: 65 outliers final: 54 residues processed: 592 average time/residue: 0.2836 time to fit residues: 261.9789 Evaluate side-chains 597 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 543 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18681 Z= 0.181 Angle : 0.597 11.857 25316 Z= 0.302 Chirality : 0.041 0.373 2857 Planarity : 0.004 0.049 3120 Dihedral : 6.019 79.958 2691 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 2.59 % Allowed : 20.87 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2221 helix: 1.57 (0.14), residues: 1371 sheet: -1.00 (0.56), residues: 76 loop : -1.30 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 372 HIS 0.004 0.001 HIS D 289 PHE 0.030 0.001 PHE C 489 TYR 0.035 0.001 TYR B 309 ARG 0.004 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 592 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 247 PHE cc_start: 0.8893 (p90) cc_final: 0.8691 (p90) REVERT: A 304 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7855 (p90) REVERT: A 420 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8350 (tpp80) REVERT: A 438 PHE cc_start: 0.9389 (t80) cc_final: 0.9070 (t80) REVERT: A 478 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 648 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 660 ILE cc_start: 0.9536 (tp) cc_final: 0.9182 (tp) REVERT: A 698 LYS cc_start: 0.9009 (mttt) cc_final: 0.8768 (mtmm) REVERT: A 717 ARG cc_start: 0.7251 (mmp-170) cc_final: 0.6612 (mmp80) REVERT: D 431 LYS cc_start: 0.8423 (tttt) cc_final: 0.8106 (mttt) REVERT: D 481 SER cc_start: 0.9131 (m) cc_final: 0.8901 (p) REVERT: D 483 SER cc_start: 0.9402 (t) cc_final: 0.9003 (p) REVERT: D 496 PHE cc_start: 0.8245 (t80) cc_final: 0.7771 (m-10) REVERT: D 526 SER cc_start: 0.9393 (t) cc_final: 0.9038 (p) REVERT: D 547 MET cc_start: 0.8347 (mmm) cc_final: 0.8091 (mmm) REVERT: D 562 MET cc_start: 0.8459 (mmm) cc_final: 0.7975 (mtt) REVERT: D 628 ASN cc_start: 0.8597 (t0) cc_final: 0.8100 (t0) REVERT: D 656 LYS cc_start: 0.9290 (tttt) cc_final: 0.9021 (ttpt) REVERT: D 743 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7677 (mtp180) REVERT: B 310 ASN cc_start: 0.9200 (t0) cc_final: 0.8988 (t0) REVERT: B 386 CYS cc_start: 0.9111 (m) cc_final: 0.8911 (m) REVERT: B 392 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8460 (mtmm) REVERT: B 472 TYR cc_start: 0.8149 (m-80) cc_final: 0.7621 (m-80) REVERT: B 478 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7653 (tm-30) REVERT: B 721 ARG cc_start: 0.7320 (mmt180) cc_final: 0.7106 (mmt180) REVERT: C 206 HIS cc_start: 0.8928 (m90) cc_final: 0.8511 (m90) REVERT: C 288 LEU cc_start: 0.9439 (mt) cc_final: 0.9190 (mt) REVERT: C 309 TYR cc_start: 0.9478 (t80) cc_final: 0.9007 (t80) REVERT: C 326 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 372 TRP cc_start: 0.8774 (p-90) cc_final: 0.8262 (p-90) REVERT: C 427 ASP cc_start: 0.8578 (m-30) cc_final: 0.8260 (m-30) REVERT: C 447 ILE cc_start: 0.9335 (mt) cc_final: 0.9125 (mt) REVERT: C 710 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8633 (tmtt) outliers start: 51 outliers final: 41 residues processed: 614 average time/residue: 0.2727 time to fit residues: 257.8009 Evaluate side-chains 607 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 564 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 0.0670 chunk 118 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18681 Z= 0.169 Angle : 0.613 12.191 25316 Z= 0.307 Chirality : 0.040 0.357 2857 Planarity : 0.004 0.048 3120 Dihedral : 5.874 78.458 2691 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.23 % Allowed : 21.79 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2221 helix: 1.51 (0.14), residues: 1367 sheet: -0.99 (0.55), residues: 76 loop : -1.31 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 372 HIS 0.004 0.000 HIS B 289 PHE 0.032 0.001 PHE A 266 TYR 0.036 0.001 TYR D 511 ARG 0.005 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 584 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 247 PHE cc_start: 0.8863 (p90) cc_final: 0.8649 (p90) REVERT: A 304 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7779 (p90) REVERT: A 372 TRP cc_start: 0.7724 (p-90) cc_final: 0.7464 (p-90) REVERT: A 420 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8342 (tpp80) REVERT: A 438 PHE cc_start: 0.9385 (t80) cc_final: 0.9069 (t80) REVERT: A 551 ASN cc_start: 0.9430 (m-40) cc_final: 0.9184 (m-40) REVERT: A 572 MET cc_start: 0.8828 (mmp) cc_final: 0.8493 (mmm) REVERT: A 648 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 660 ILE cc_start: 0.9525 (tp) cc_final: 0.9234 (tp) REVERT: A 698 LYS cc_start: 0.8998 (mttt) cc_final: 0.8759 (mtmm) REVERT: A 717 ARG cc_start: 0.7210 (mmp-170) cc_final: 0.6550 (mmp80) REVERT: D 431 LYS cc_start: 0.8451 (tttt) cc_final: 0.8136 (mttt) REVERT: D 481 SER cc_start: 0.9146 (m) cc_final: 0.8923 (p) REVERT: D 483 SER cc_start: 0.9398 (t) cc_final: 0.8995 (p) REVERT: D 496 PHE cc_start: 0.8163 (t80) cc_final: 0.7761 (m-10) REVERT: D 499 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7868 (tpp80) REVERT: D 526 SER cc_start: 0.9407 (t) cc_final: 0.9006 (p) REVERT: D 628 ASN cc_start: 0.8528 (t0) cc_final: 0.8048 (t0) REVERT: D 656 LYS cc_start: 0.9274 (tttt) cc_final: 0.9021 (ttpt) REVERT: D 743 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7846 (mtp180) REVERT: B 392 LYS cc_start: 0.8764 (ptpt) cc_final: 0.8397 (mtmm) REVERT: B 472 TYR cc_start: 0.8129 (m-80) cc_final: 0.7600 (m-80) REVERT: B 478 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 288 LEU cc_start: 0.9422 (mt) cc_final: 0.9174 (mt) REVERT: C 309 TYR cc_start: 0.9483 (t80) cc_final: 0.9006 (t80) REVERT: C 326 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7408 (mt-10) REVERT: C 372 TRP cc_start: 0.8779 (p-90) cc_final: 0.8246 (p-90) REVERT: C 427 ASP cc_start: 0.8599 (m-30) cc_final: 0.8321 (m-30) REVERT: C 447 ILE cc_start: 0.9318 (mt) cc_final: 0.9108 (mt) REVERT: C 710 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8635 (tmtt) outliers start: 44 outliers final: 40 residues processed: 605 average time/residue: 0.2748 time to fit residues: 256.5970 Evaluate side-chains 607 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 565 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 145 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 134 optimal weight: 0.0040 chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 18681 Z= 0.155 Angle : 0.620 11.886 25316 Z= 0.308 Chirality : 0.040 0.373 2857 Planarity : 0.003 0.046 3120 Dihedral : 5.684 75.803 2691 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.03 % Allowed : 22.35 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2221 helix: 1.44 (0.14), residues: 1371 sheet: -0.95 (0.56), residues: 76 loop : -1.31 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 372 HIS 0.004 0.001 HIS B 289 PHE 0.035 0.001 PHE D 369 TYR 0.043 0.001 TYR D 511 ARG 0.004 0.000 ARG C 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 602 time to evaluate : 2.127 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 247 PHE cc_start: 0.8808 (p90) cc_final: 0.8592 (p90) REVERT: A 372 TRP cc_start: 0.7723 (p-90) cc_final: 0.7473 (p-90) REVERT: A 420 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8386 (tpp80) REVERT: A 438 PHE cc_start: 0.9375 (t80) cc_final: 0.9095 (t80) REVERT: A 648 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 660 ILE cc_start: 0.9506 (tp) cc_final: 0.9215 (tp) REVERT: A 698 LYS cc_start: 0.8981 (mttt) cc_final: 0.8741 (mtmm) REVERT: A 717 ARG cc_start: 0.7184 (mmp-170) cc_final: 0.6543 (mmp80) REVERT: A 746 GLU cc_start: 0.8349 (mp0) cc_final: 0.8141 (mp0) REVERT: D 431 LYS cc_start: 0.8523 (tttt) cc_final: 0.8170 (mttt) REVERT: D 481 SER cc_start: 0.9196 (m) cc_final: 0.8963 (p) REVERT: D 483 SER cc_start: 0.9389 (t) cc_final: 0.8990 (p) REVERT: D 496 PHE cc_start: 0.8112 (t80) cc_final: 0.7726 (m-10) REVERT: D 499 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7864 (tpp80) REVERT: D 526 SER cc_start: 0.9335 (t) cc_final: 0.8988 (p) REVERT: D 547 MET cc_start: 0.8199 (mmm) cc_final: 0.7965 (mmm) REVERT: D 628 ASN cc_start: 0.8418 (t0) cc_final: 0.7954 (t0) REVERT: D 639 LYS cc_start: 0.9007 (mttt) cc_final: 0.8757 (mtmt) REVERT: D 656 LYS cc_start: 0.9245 (tttt) cc_final: 0.9009 (ttpt) REVERT: D 743 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7917 (mtp180) REVERT: B 392 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8357 (mtmm) REVERT: B 428 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7766 (mtm180) REVERT: B 472 TYR cc_start: 0.8135 (m-80) cc_final: 0.7601 (m-80) REVERT: B 478 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 200 LYS cc_start: 0.7472 (tppt) cc_final: 0.7220 (tppt) REVERT: C 288 LEU cc_start: 0.9420 (mt) cc_final: 0.9171 (mt) REVERT: C 309 TYR cc_start: 0.9486 (t80) cc_final: 0.8947 (t80) REVERT: C 326 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7360 (mt-10) REVERT: C 372 TRP cc_start: 0.8774 (p-90) cc_final: 0.8307 (p-90) REVERT: C 427 ASP cc_start: 0.8565 (m-30) cc_final: 0.8298 (m-30) REVERT: C 447 ILE cc_start: 0.9303 (mt) cc_final: 0.9095 (mt) REVERT: C 710 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8646 (tmtt) outliers start: 40 outliers final: 37 residues processed: 623 average time/residue: 0.2717 time to fit residues: 262.3465 Evaluate side-chains 618 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 580 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 48 optimal weight: 0.0980 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 393 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097074 restraints weight = 36975.268| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.38 r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18681 Z= 0.167 Angle : 0.629 12.560 25316 Z= 0.313 Chirality : 0.041 0.347 2857 Planarity : 0.003 0.046 3120 Dihedral : 5.576 74.257 2691 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.98 % Allowed : 23.01 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.64 (0.18), residues: 2221 helix: 1.44 (0.14), residues: 1367 sheet: -0.92 (0.56), residues: 76 loop : -1.27 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 372 HIS 0.004 0.001 HIS C 206 PHE 0.034 0.001 PHE D 369 TYR 0.044 0.001 TYR B 309 ARG 0.004 0.000 ARG C 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5374.10 seconds wall clock time: 97 minutes 44.24 seconds (5864.24 seconds total)