Starting phenix.real_space_refine on Sun Mar 17 10:35:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzd_24090/03_2024/7mzd_24090_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzd_24090/03_2024/7mzd_24090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzd_24090/03_2024/7mzd_24090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzd_24090/03_2024/7mzd_24090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzd_24090/03_2024/7mzd_24090_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzd_24090/03_2024/7mzd_24090_updated.pdb" } resolution = 2.9 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 Na 2 4.78 5 C 11488 2.51 5 N 2800 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17486 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "D" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "B" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "C" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' NA': 2, '6EU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.63, per 1000 atoms: 0.55 Number of scatterers: 17486 At special positions: 0 Unit cell: (125.934, 125.934, 112.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 Na 2 11.00 O 3096 8.00 N 2800 7.00 C 11488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 3.3 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 4 sheets defined 59.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 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 409 through 414 removed outlier: 4.445A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.265A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.152A 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: 4.078A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 577 through 598 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.948A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 684 removed outlier: 4.078A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 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 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.482A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.749A 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: 5.343A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.179A 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: 4.070A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 575 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.039A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 684 removed outlier: 4.280A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 711 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 293 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 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.471A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 414' Processing helix chain 'B' and resid 416 through 453 removed outlier: 5.360A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.206A 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: 4.070A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.883A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 684 removed outlier: 4.097A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.431A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 416 through 453 removed outlier: 5.275A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.133A 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: 4.074A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.714A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.025A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 684 removed outlier: 4.076A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.253A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.352A 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: 6.386A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.419A 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: 3.569A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.406A 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: 6.384A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2701 1.31 - 1.44: 5136 1.44 - 1.57: 9903 1.57 - 1.70: 20 1.70 - 1.83: 164 Bond restraints: 17924 Sorted by residual: bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.199 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.521 -0.191 2.00e-02 2.50e+03 9.09e+01 ... (remaining 17919 not shown) Histogram of bond angle deviations from ideal: 97.66 - 104.93: 223 104.93 - 112.20: 8839 112.20 - 119.47: 5977 119.47 - 126.74: 9066 126.74 - 134.01: 215 Bond angle restraints: 24320 Sorted by residual: angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAO 6EU A 901 " ideal model delta sigma weight residual 115.38 130.03 -14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 129.98 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 129.91 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 129.88 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 ... (remaining 24315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10267 17.95 - 35.90: 416 35.90 - 53.85: 96 53.85 - 71.80: 9 71.80 - 89.75: 11 Dihedral angle restraints: 10799 sinusoidal: 4531 harmonic: 6268 Sorted by residual: dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE B 712 " pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 10796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2697 0.127 - 0.254: 15 0.254 - 0.382: 4 0.382 - 0.509: 8 0.509 - 0.636: 4 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CAJ 6EU A 901 " pdb=" CAK 6EU A 901 " pdb=" CAN 6EU A 901 " pdb=" CAO 6EU A 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CAJ 6EU C 901 " pdb=" CAK 6EU C 901 " pdb=" CAN 6EU C 901 " pdb=" CAO 6EU C 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.63 2.00e-01 2.50e+01 9.99e+00 ... (remaining 2725 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " -0.098 2.00e-02 2.50e+03 1.72e-01 2.96e+02 pdb=" CAV 6EU B 901 " 0.298 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " -0.100 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " 0.098 2.00e-02 2.50e+03 1.72e-01 2.95e+02 pdb=" CAV 6EU D 901 " -0.298 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " 0.100 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " -0.098 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" CAV 6EU A 901 " 0.297 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " -0.100 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " -0.099 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3781 2.78 - 3.31: 17501 3.31 - 3.84: 29225 3.84 - 4.37: 34758 4.37 - 4.90: 59160 Nonbonded interactions: 144425 Sorted by model distance: nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.299 2.440 nonbonded pdb=" O GLY A 643 " pdb="NA NA A 902 " model vdw 2.334 2.470 nonbonded pdb=" O GLY B 643 " pdb="NA NA A 902 " model vdw 2.336 2.470 nonbonded pdb=" O GLY C 643 " pdb="NA NA A 902 " model vdw 2.341 2.470 ... (remaining 144420 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 198 through 752 or resid 901)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.990 Check model and map are aligned: 0.290 Set scattering table: 0.150 Process input model: 46.360 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 0.223 17924 Z= 0.620 Angle : 0.791 14.649 24320 Z= 0.380 Chirality : 0.053 0.636 2728 Planarity : 0.007 0.172 2992 Dihedral : 10.897 89.753 6772 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.59 % Allowed : 0.48 % Favored : 98.94 % 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: 1.32 (0.18), residues: 2120 helix: 2.09 (0.14), residues: 1288 sheet: -0.44 (0.50), residues: 84 loop : -1.19 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 749 HIS 0.002 0.001 HIS B 289 PHE 0.022 0.002 PHE C 304 TYR 0.012 0.001 TYR A 511 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 646 time to evaluate : 1.817 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 260 GLN cc_start: 0.8511 (mt0) cc_final: 0.8123 (mt0) REVERT: A 272 TRP cc_start: 0.8323 (m-90) cc_final: 0.7971 (m-90) REVERT: A 273 GLN cc_start: 0.8249 (tp40) cc_final: 0.7927 (tp-100) REVERT: A 378 HIS cc_start: 0.8189 (p-80) cc_final: 0.7858 (p90) REVERT: A 383 ASP cc_start: 0.7822 (t0) cc_final: 0.7534 (t0) REVERT: A 385 SER cc_start: 0.8469 (t) cc_final: 0.8167 (m) REVERT: A 406 THR cc_start: 0.8613 (m) cc_final: 0.8398 (m) REVERT: A 408 ASN cc_start: 0.8321 (m-40) cc_final: 0.8050 (m-40) REVERT: A 506 LEU cc_start: 0.9157 (tp) cc_final: 0.8866 (tp) REVERT: A 536 GLU cc_start: 0.8833 (mp0) cc_final: 0.8617 (mp0) REVERT: A 741 CYS cc_start: 0.8321 (m) cc_final: 0.8074 (m) REVERT: A 748 ASN cc_start: 0.9077 (t0) cc_final: 0.8718 (t0) REVERT: D 273 GLN cc_start: 0.8142 (tp40) cc_final: 0.7887 (tp-100) REVERT: D 378 HIS cc_start: 0.8374 (p-80) cc_final: 0.8065 (p90) REVERT: D 385 SER cc_start: 0.8941 (t) cc_final: 0.8615 (m) REVERT: D 506 LEU cc_start: 0.9194 (tp) cc_final: 0.8886 (tp) REVERT: D 509 ASP cc_start: 0.7833 (t0) cc_final: 0.7511 (t0) REVERT: D 536 GLU cc_start: 0.8834 (mp0) cc_final: 0.8612 (mp0) REVERT: D 748 ASN cc_start: 0.9053 (t0) cc_final: 0.8736 (t0) REVERT: B 260 GLN cc_start: 0.8485 (mt0) cc_final: 0.8153 (mt0) REVERT: B 266 PHE cc_start: 0.8500 (t80) cc_final: 0.8138 (t80) REVERT: B 378 HIS cc_start: 0.8150 (p-80) cc_final: 0.7851 (p90) REVERT: B 385 SER cc_start: 0.8607 (t) cc_final: 0.8304 (m) REVERT: B 506 LEU cc_start: 0.9180 (tp) cc_final: 0.8882 (tp) REVERT: B 509 ASP cc_start: 0.7866 (t0) cc_final: 0.7477 (t0) REVERT: B 536 GLU cc_start: 0.8838 (mp0) cc_final: 0.8630 (mp0) REVERT: B 748 ASN cc_start: 0.9068 (t0) cc_final: 0.8719 (t0) REVERT: C 260 GLN cc_start: 0.8506 (mt0) cc_final: 0.8124 (mt0) REVERT: C 266 PHE cc_start: 0.8476 (t80) cc_final: 0.8224 (t80) REVERT: C 378 HIS cc_start: 0.8404 (p-80) cc_final: 0.8065 (p90) REVERT: C 383 ASP cc_start: 0.7912 (t0) cc_final: 0.7556 (t0) REVERT: C 385 SER cc_start: 0.8883 (t) cc_final: 0.8581 (m) REVERT: C 406 THR cc_start: 0.8623 (m) cc_final: 0.8402 (m) REVERT: C 506 LEU cc_start: 0.9176 (tp) cc_final: 0.8863 (tp) REVERT: C 536 GLU cc_start: 0.8826 (mp0) cc_final: 0.8624 (mp0) REVERT: C 741 CYS cc_start: 0.8420 (m) cc_final: 0.8150 (m) REVERT: C 748 ASN cc_start: 0.8974 (t0) cc_final: 0.8717 (t0) outliers start: 11 outliers final: 0 residues processed: 649 average time/residue: 1.2416 time to fit residues: 896.6339 Evaluate side-chains 412 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.0030 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 393 ASN A 408 ASN A 560 GLN D 206 HIS D 228 GLN D 260 GLN D 393 ASN B 206 HIS B 228 GLN B 269 GLN B 310 ASN B 560 GLN B 561 GLN C 206 HIS C 310 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17924 Z= 0.196 Angle : 0.568 10.144 24320 Z= 0.290 Chirality : 0.039 0.160 2728 Planarity : 0.004 0.042 2992 Dihedral : 7.324 59.959 2720 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.87 % Allowed : 12.71 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2120 helix: 2.27 (0.14), residues: 1288 sheet: -0.35 (0.53), residues: 84 loop : -1.28 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 272 HIS 0.004 0.001 HIS B 364 PHE 0.016 0.001 PHE D 489 TYR 0.010 0.001 TYR D 627 ARG 0.007 0.001 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 446 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7420 (mp-120) REVERT: A 272 TRP cc_start: 0.7979 (m-90) cc_final: 0.7574 (m-90) REVERT: A 273 GLN cc_start: 0.8307 (tp40) cc_final: 0.7853 (tp40) REVERT: A 383 ASP cc_start: 0.7922 (t0) cc_final: 0.7513 (t0) REVERT: A 499 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.8019 (mpt180) REVERT: A 741 CYS cc_start: 0.8366 (m) cc_final: 0.8160 (m) REVERT: A 748 ASN cc_start: 0.9053 (t0) cc_final: 0.8727 (t0) REVERT: D 214 MET cc_start: 0.8259 (tpt) cc_final: 0.7793 (tpt) REVERT: D 228 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7321 (mp-120) REVERT: D 272 TRP cc_start: 0.8451 (m-90) cc_final: 0.8200 (m-90) REVERT: D 273 GLN cc_start: 0.8171 (tp40) cc_final: 0.7861 (tp40) REVERT: D 293 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 748 ASN cc_start: 0.9075 (t0) cc_final: 0.8776 (t0) REVERT: B 228 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7449 (mp-120) REVERT: B 246 TYR cc_start: 0.8894 (t80) cc_final: 0.8592 (t80) REVERT: B 260 GLN cc_start: 0.8406 (mt0) cc_final: 0.8126 (mt0) REVERT: B 315 LEU cc_start: 0.9239 (mm) cc_final: 0.8922 (mt) REVERT: B 383 ASP cc_start: 0.7883 (t0) cc_final: 0.7656 (t0) REVERT: B 676 ASN cc_start: 0.9356 (m-40) cc_final: 0.8664 (m-40) REVERT: B 748 ASN cc_start: 0.9110 (t0) cc_final: 0.8805 (t0) REVERT: C 293 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8353 (mm-30) REVERT: C 315 LEU cc_start: 0.9240 (mm) cc_final: 0.8895 (mt) REVERT: C 383 ASP cc_start: 0.7928 (t0) cc_final: 0.7528 (t0) REVERT: C 741 CYS cc_start: 0.8406 (m) cc_final: 0.8202 (m) outliers start: 54 outliers final: 22 residues processed: 468 average time/residue: 1.0963 time to fit residues: 579.8527 Evaluate side-chains 418 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 393 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 0.0670 chunk 171 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN D 228 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 269 GLN B 378 HIS ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS C 260 GLN C 310 ASN C 408 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17924 Z= 0.256 Angle : 0.583 14.051 24320 Z= 0.294 Chirality : 0.039 0.146 2728 Planarity : 0.004 0.041 2992 Dihedral : 7.339 59.839 2720 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.30 % Allowed : 14.89 % Favored : 81.81 % 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: 1.36 (0.19), residues: 2120 helix: 2.18 (0.14), residues: 1284 sheet: -0.44 (0.52), residues: 84 loop : -1.29 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 372 HIS 0.004 0.001 HIS B 378 PHE 0.015 0.001 PHE B 304 TYR 0.011 0.001 TYR D 374 ARG 0.007 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 417 time to evaluate : 1.993 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 272 TRP cc_start: 0.8134 (m-90) cc_final: 0.7705 (m-90) REVERT: A 273 GLN cc_start: 0.8299 (tp40) cc_final: 0.7827 (tp40) REVERT: A 293 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 327 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 378 HIS cc_start: 0.8377 (p90) cc_final: 0.7864 (p90) REVERT: A 420 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8077 (mmm-85) REVERT: A 471 ASP cc_start: 0.8218 (m-30) cc_final: 0.7969 (t0) REVERT: A 738 TYR cc_start: 0.8436 (m-80) cc_final: 0.8126 (m-80) REVERT: D 214 MET cc_start: 0.8206 (tpt) cc_final: 0.7759 (tpt) REVERT: D 246 TYR cc_start: 0.8969 (t80) cc_final: 0.8728 (t80) REVERT: D 273 GLN cc_start: 0.8195 (tp40) cc_final: 0.7814 (tp40) REVERT: D 293 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8335 (mm-30) REVERT: D 429 PHE cc_start: 0.8058 (t80) cc_final: 0.7812 (t80) REVERT: D 716 MET cc_start: 0.4666 (mpp) cc_final: 0.3956 (tpp) REVERT: D 748 ASN cc_start: 0.9105 (t0) cc_final: 0.8793 (t0) REVERT: B 246 TYR cc_start: 0.8934 (t80) cc_final: 0.8601 (t80) REVERT: B 293 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8386 (mm-30) REVERT: B 315 LEU cc_start: 0.9217 (mm) cc_final: 0.8912 (mt) REVERT: B 324 LYS cc_start: 0.8726 (mttp) cc_final: 0.8498 (ptpp) REVERT: B 327 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 383 ASP cc_start: 0.7830 (t0) cc_final: 0.7629 (t0) REVERT: B 748 ASN cc_start: 0.9149 (t0) cc_final: 0.8858 (t0) REVERT: C 246 TYR cc_start: 0.8942 (t80) cc_final: 0.8705 (t80) REVERT: C 273 GLN cc_start: 0.8104 (tp40) cc_final: 0.7764 (tp-100) REVERT: C 293 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8358 (mm-30) REVERT: C 315 LEU cc_start: 0.9231 (mm) cc_final: 0.8882 (mt) REVERT: C 324 LYS cc_start: 0.8716 (mttp) cc_final: 0.8485 (ptpp) REVERT: C 327 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7322 (mt-10) REVERT: C 428 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7809 (ttm-80) outliers start: 62 outliers final: 31 residues processed: 442 average time/residue: 1.1370 time to fit residues: 566.0071 Evaluate side-chains 432 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 401 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 129 optimal weight: 0.0570 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 408 ASN B 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17924 Z= 0.217 Angle : 0.567 14.086 24320 Z= 0.284 Chirality : 0.039 0.158 2728 Planarity : 0.004 0.043 2992 Dihedral : 7.192 59.962 2720 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.09 % Allowed : 16.91 % Favored : 80.00 % 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: 1.39 (0.19), residues: 2120 helix: 2.21 (0.14), residues: 1288 sheet: 0.34 (0.58), residues: 56 loop : -1.35 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 272 HIS 0.005 0.001 HIS B 364 PHE 0.014 0.001 PHE B 304 TYR 0.011 0.001 TYR D 374 ARG 0.008 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 417 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.8937 (t80) cc_final: 0.8654 (t80) REVERT: A 272 TRP cc_start: 0.8168 (m-90) cc_final: 0.7811 (m-90) REVERT: A 273 GLN cc_start: 0.8297 (tp40) cc_final: 0.7825 (tp40) REVERT: A 293 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 378 HIS cc_start: 0.8364 (p90) cc_final: 0.7799 (p90) REVERT: A 420 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8050 (mmm-85) REVERT: A 471 ASP cc_start: 0.8237 (m-30) cc_final: 0.7936 (t0) REVERT: A 748 ASN cc_start: 0.9076 (t0) cc_final: 0.8739 (t0) REVERT: D 214 MET cc_start: 0.8135 (tpt) cc_final: 0.7744 (tpt) REVERT: D 246 TYR cc_start: 0.8995 (t80) cc_final: 0.8719 (t80) REVERT: D 271 SER cc_start: 0.8587 (m) cc_final: 0.8253 (p) REVERT: D 272 TRP cc_start: 0.8057 (m-90) cc_final: 0.7663 (m-90) REVERT: D 273 GLN cc_start: 0.8210 (tp40) cc_final: 0.7843 (tp40) REVERT: D 293 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8361 (mm-30) REVERT: D 360 PRO cc_start: 0.9114 (Cg_exo) cc_final: 0.8881 (Cg_endo) REVERT: D 429 PHE cc_start: 0.8016 (t80) cc_final: 0.7763 (t80) REVERT: D 471 ASP cc_start: 0.8194 (m-30) cc_final: 0.7905 (t0) REVERT: D 572 MET cc_start: 0.8891 (ttm) cc_final: 0.8671 (ttp) REVERT: D 748 ASN cc_start: 0.9133 (t0) cc_final: 0.8819 (t0) REVERT: B 246 TYR cc_start: 0.8936 (t80) cc_final: 0.8649 (t80) REVERT: B 273 GLN cc_start: 0.8128 (tp40) cc_final: 0.7755 (tp-100) REVERT: B 293 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8396 (mm-30) REVERT: B 315 LEU cc_start: 0.9226 (mm) cc_final: 0.8883 (mt) REVERT: B 327 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 383 ASP cc_start: 0.7872 (t0) cc_final: 0.7607 (t0) REVERT: B 748 ASN cc_start: 0.9149 (t0) cc_final: 0.8841 (t0) REVERT: C 246 TYR cc_start: 0.8990 (t80) cc_final: 0.8704 (t80) REVERT: C 293 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8394 (mm-30) REVERT: C 315 LEU cc_start: 0.9237 (mm) cc_final: 0.8879 (mt) REVERT: C 327 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 710 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8642 (ttpp) outliers start: 58 outliers final: 29 residues processed: 440 average time/residue: 1.1166 time to fit residues: 555.3416 Evaluate side-chains 412 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 383 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 560 GLN C 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17924 Z= 0.283 Angle : 0.593 14.766 24320 Z= 0.299 Chirality : 0.040 0.147 2728 Planarity : 0.004 0.043 2992 Dihedral : 7.144 58.285 2720 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.19 % Allowed : 18.24 % Favored : 78.56 % 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: 1.24 (0.18), residues: 2120 helix: 2.12 (0.14), residues: 1288 sheet: -0.48 (0.53), residues: 76 loop : -1.40 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.004 0.001 HIS B 378 PHE 0.016 0.001 PHE A 304 TYR 0.014 0.001 TYR B 374 ARG 0.007 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 398 time to evaluate : 2.029 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 228 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7271 (mp-120) REVERT: A 246 TYR cc_start: 0.9000 (t80) cc_final: 0.8722 (t80) REVERT: A 272 TRP cc_start: 0.8167 (m-90) cc_final: 0.7763 (m-90) REVERT: A 273 GLN cc_start: 0.8320 (tp40) cc_final: 0.7832 (tp40) REVERT: A 293 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8420 (mm-30) REVERT: A 378 HIS cc_start: 0.8307 (p90) cc_final: 0.7833 (p90) REVERT: A 420 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8021 (mmm-85) REVERT: A 471 ASP cc_start: 0.8278 (m-30) cc_final: 0.7984 (t0) REVERT: A 572 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8622 (ttp) REVERT: D 214 MET cc_start: 0.8138 (tpt) cc_final: 0.7759 (tpt) REVERT: D 246 TYR cc_start: 0.9057 (t80) cc_final: 0.8788 (t80) REVERT: D 271 SER cc_start: 0.8741 (m) cc_final: 0.8509 (p) REVERT: D 272 TRP cc_start: 0.8040 (m-90) cc_final: 0.7801 (m-90) REVERT: D 273 GLN cc_start: 0.8179 (tp40) cc_final: 0.7754 (tp40) REVERT: D 293 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 360 PRO cc_start: 0.9191 (Cg_exo) cc_final: 0.8963 (Cg_endo) REVERT: D 471 ASP cc_start: 0.8204 (m-30) cc_final: 0.7949 (t0) REVERT: D 738 TYR cc_start: 0.8293 (m-10) cc_final: 0.8072 (m-10) REVERT: D 748 ASN cc_start: 0.9127 (t0) cc_final: 0.8816 (t0) REVERT: B 214 MET cc_start: 0.8119 (tpt) cc_final: 0.7707 (tpt) REVERT: B 246 TYR cc_start: 0.8996 (t80) cc_final: 0.8658 (t80) REVERT: B 273 GLN cc_start: 0.8132 (tp40) cc_final: 0.7765 (tp40) REVERT: B 293 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 383 ASP cc_start: 0.7848 (t0) cc_final: 0.7567 (t0) REVERT: B 748 ASN cc_start: 0.9171 (t0) cc_final: 0.8849 (t0) REVERT: C 214 MET cc_start: 0.8074 (tpt) cc_final: 0.7629 (tpt) REVERT: C 246 TYR cc_start: 0.9064 (t80) cc_final: 0.8756 (t80) REVERT: C 293 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8378 (mm-30) REVERT: C 315 LEU cc_start: 0.9237 (mm) cc_final: 0.8872 (mt) REVERT: C 324 LYS cc_start: 0.8630 (ptpp) cc_final: 0.8259 (mtmm) REVERT: C 710 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8654 (ttpp) outliers start: 60 outliers final: 32 residues processed: 418 average time/residue: 1.0462 time to fit residues: 496.8378 Evaluate side-chains 414 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 380 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 GLN D 561 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17924 Z= 0.331 Angle : 0.617 16.316 24320 Z= 0.310 Chirality : 0.041 0.149 2728 Planarity : 0.004 0.043 2992 Dihedral : 7.066 56.284 2720 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.24 % Allowed : 18.99 % Favored : 77.77 % 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: 1.22 (0.18), residues: 2120 helix: 2.12 (0.14), residues: 1264 sheet: -0.55 (0.53), residues: 76 loop : -1.32 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 272 HIS 0.005 0.001 HIS A 364 PHE 0.017 0.001 PHE B 730 TYR 0.013 0.002 TYR C 627 ARG 0.005 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 388 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7237 (mp-120) REVERT: A 272 TRP cc_start: 0.8206 (m-90) cc_final: 0.7745 (m-90) REVERT: A 273 GLN cc_start: 0.8329 (tp40) cc_final: 0.7777 (tp40) REVERT: A 293 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8414 (mm-30) REVERT: A 324 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8259 (ptpp) REVERT: A 327 GLU cc_start: 0.7720 (pp20) cc_final: 0.7179 (pp20) REVERT: A 378 HIS cc_start: 0.8291 (p90) cc_final: 0.7244 (p90) REVERT: A 420 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8125 (mmt90) REVERT: A 471 ASP cc_start: 0.8253 (m-30) cc_final: 0.8001 (t0) REVERT: A 682 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7660 (mtm) REVERT: D 214 MET cc_start: 0.8064 (tpt) cc_final: 0.7769 (tpt) REVERT: D 246 TYR cc_start: 0.9090 (t80) cc_final: 0.8817 (t80) REVERT: D 271 SER cc_start: 0.8773 (m) cc_final: 0.8570 (p) REVERT: D 273 GLN cc_start: 0.8209 (tp40) cc_final: 0.7745 (tp40) REVERT: D 293 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8374 (mm-30) REVERT: D 445 MET cc_start: 0.9164 (mmm) cc_final: 0.8947 (mmm) REVERT: D 471 ASP cc_start: 0.8281 (m-30) cc_final: 0.8027 (t0) REVERT: D 738 TYR cc_start: 0.8367 (m-10) cc_final: 0.8100 (m-10) REVERT: D 748 ASN cc_start: 0.9130 (t0) cc_final: 0.8814 (t0) REVERT: B 214 MET cc_start: 0.8001 (tpt) cc_final: 0.7600 (tpt) REVERT: B 246 TYR cc_start: 0.9063 (t80) cc_final: 0.8756 (t80) REVERT: B 273 GLN cc_start: 0.8137 (tp40) cc_final: 0.7728 (tp40) REVERT: B 293 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8360 (mm-30) REVERT: B 445 MET cc_start: 0.9167 (mmm) cc_final: 0.8951 (mmm) REVERT: B 748 ASN cc_start: 0.9154 (t0) cc_final: 0.8843 (t0) REVERT: C 214 MET cc_start: 0.8008 (tpt) cc_final: 0.7652 (tpt) REVERT: C 246 TYR cc_start: 0.9091 (t80) cc_final: 0.8775 (t80) REVERT: C 293 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 315 LEU cc_start: 0.9242 (mm) cc_final: 0.8877 (mt) REVERT: C 324 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8347 (ptpp) REVERT: C 710 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8654 (ttpp) outliers start: 61 outliers final: 37 residues processed: 412 average time/residue: 1.1031 time to fit residues: 514.8926 Evaluate side-chains 413 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 373 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17924 Z= 0.169 Angle : 0.579 15.127 24320 Z= 0.286 Chirality : 0.038 0.156 2728 Planarity : 0.004 0.043 2992 Dihedral : 6.343 50.703 2720 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.97 % Allowed : 21.28 % Favored : 76.76 % 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: 1.50 (0.19), residues: 2120 helix: 2.35 (0.14), residues: 1260 sheet: -0.41 (0.56), residues: 76 loop : -1.19 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 272 HIS 0.004 0.001 HIS B 378 PHE 0.028 0.001 PHE C 730 TYR 0.012 0.001 TYR D 374 ARG 0.006 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 427 time to evaluate : 2.092 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 246 TYR cc_start: 0.9000 (t80) cc_final: 0.8741 (t80) REVERT: A 273 GLN cc_start: 0.8322 (tp40) cc_final: 0.7856 (tp40) REVERT: A 293 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 324 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8185 (ptpp) REVERT: A 327 GLU cc_start: 0.7675 (pp20) cc_final: 0.7077 (pp20) REVERT: A 420 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: A 460 LEU cc_start: 0.8461 (mm) cc_final: 0.8147 (mt) REVERT: A 471 ASP cc_start: 0.8223 (m-30) cc_final: 0.7960 (t0) REVERT: D 214 MET cc_start: 0.7993 (tpt) cc_final: 0.7766 (tpt) REVERT: D 246 TYR cc_start: 0.9034 (t80) cc_final: 0.8769 (t80) REVERT: D 273 GLN cc_start: 0.8204 (tp40) cc_final: 0.7811 (tp40) REVERT: D 293 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8403 (mm-30) REVERT: D 315 LEU cc_start: 0.9226 (mt) cc_final: 0.8908 (tt) REVERT: D 360 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.9018 (Cg_endo) REVERT: D 391 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 471 ASP cc_start: 0.8229 (m-30) cc_final: 0.7972 (t0) REVERT: D 738 TYR cc_start: 0.8239 (m-10) cc_final: 0.7926 (m-10) REVERT: B 214 MET cc_start: 0.7934 (tpt) cc_final: 0.7576 (tpt) REVERT: B 246 TYR cc_start: 0.8983 (t80) cc_final: 0.8613 (t80) REVERT: B 293 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8362 (mm-30) REVERT: B 324 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8284 (ptpp) REVERT: B 748 ASN cc_start: 0.9145 (t0) cc_final: 0.8848 (t0) REVERT: C 214 MET cc_start: 0.7897 (tpt) cc_final: 0.7531 (tpt) REVERT: C 246 TYR cc_start: 0.9065 (t80) cc_final: 0.8728 (t80) REVERT: C 293 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8382 (mm-30) REVERT: C 315 LEU cc_start: 0.9229 (mm) cc_final: 0.8809 (mt) REVERT: C 710 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8610 (ttpp) outliers start: 37 outliers final: 20 residues processed: 442 average time/residue: 1.0349 time to fit residues: 519.9180 Evaluate side-chains 405 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 385 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 741 CYS 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 C residue 215 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS C 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17924 Z= 0.185 Angle : 0.602 15.415 24320 Z= 0.295 Chirality : 0.038 0.152 2728 Planarity : 0.004 0.045 2992 Dihedral : 5.631 40.021 2720 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.97 % Allowed : 21.97 % Favored : 76.06 % 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: 1.49 (0.19), residues: 2120 helix: 2.31 (0.14), residues: 1264 sheet: -0.50 (0.56), residues: 76 loop : -1.16 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 272 HIS 0.004 0.001 HIS B 378 PHE 0.019 0.001 PHE C 730 TYR 0.012 0.001 TYR D 374 ARG 0.006 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 403 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.9010 (t80) cc_final: 0.8683 (t80) REVERT: A 273 GLN cc_start: 0.8355 (tp40) cc_final: 0.7937 (tp40) REVERT: A 293 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 324 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8134 (ptpp) REVERT: A 327 GLU cc_start: 0.7687 (pp20) cc_final: 0.7108 (pp20) REVERT: A 420 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: A 460 LEU cc_start: 0.8522 (mm) cc_final: 0.8192 (mt) REVERT: D 214 MET cc_start: 0.7974 (tpt) cc_final: 0.7666 (tpt) REVERT: D 246 TYR cc_start: 0.9034 (t80) cc_final: 0.8776 (t80) REVERT: D 273 GLN cc_start: 0.8213 (tp40) cc_final: 0.7833 (tp40) REVERT: D 293 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8389 (mm-30) REVERT: D 315 LEU cc_start: 0.9224 (mt) cc_final: 0.8902 (tt) REVERT: D 360 PRO cc_start: 0.9248 (Cg_exo) cc_final: 0.9044 (Cg_endo) REVERT: D 471 ASP cc_start: 0.8227 (m-30) cc_final: 0.7989 (t0) REVERT: D 738 TYR cc_start: 0.8192 (m-10) cc_final: 0.7883 (m-10) REVERT: D 748 ASN cc_start: 0.9130 (t0) cc_final: 0.8808 (t0) REVERT: B 246 TYR cc_start: 0.9014 (t80) cc_final: 0.8673 (t80) REVERT: B 293 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 324 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8359 (ptpp) REVERT: B 383 ASP cc_start: 0.7866 (t0) cc_final: 0.7615 (t0) REVERT: B 748 ASN cc_start: 0.9141 (t0) cc_final: 0.8855 (t0) REVERT: C 214 MET cc_start: 0.7738 (tpt) cc_final: 0.7447 (tpt) REVERT: C 246 TYR cc_start: 0.9074 (t80) cc_final: 0.8755 (t80) REVERT: C 293 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8406 (mm-30) REVERT: C 315 LEU cc_start: 0.9214 (mm) cc_final: 0.8730 (mt) outliers start: 37 outliers final: 23 residues processed: 418 average time/residue: 0.9880 time to fit residues: 474.5348 Evaluate side-chains 411 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 388 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 741 CYS 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 674 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 5.9990 chunk 178 optimal weight: 0.0770 chunk 190 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 189 optimal weight: 4.9990 chunk 125 optimal weight: 0.0670 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 676 ASN C 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17924 Z= 0.177 Angle : 0.606 16.521 24320 Z= 0.294 Chirality : 0.038 0.158 2728 Planarity : 0.004 0.045 2992 Dihedral : 5.068 29.696 2720 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.49 % Allowed : 22.87 % Favored : 75.64 % 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: 1.53 (0.19), residues: 2120 helix: 2.34 (0.14), residues: 1264 sheet: -0.61 (0.55), residues: 76 loop : -1.12 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 272 HIS 0.004 0.001 HIS A 378 PHE 0.016 0.001 PHE C 730 TYR 0.012 0.001 TYR D 374 ARG 0.006 0.000 ARG D 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 411 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.9021 (t80) cc_final: 0.8703 (t80) REVERT: A 273 GLN cc_start: 0.8320 (tp40) cc_final: 0.7879 (tp40) REVERT: A 293 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 324 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8171 (ptpp) REVERT: A 327 GLU cc_start: 0.7689 (pp20) cc_final: 0.7104 (pp20) REVERT: A 420 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8062 (mmm-85) REVERT: A 460 LEU cc_start: 0.8493 (mm) cc_final: 0.8154 (mt) REVERT: A 471 ASP cc_start: 0.8266 (m-30) cc_final: 0.7851 (t0) REVERT: D 214 MET cc_start: 0.7914 (tpt) cc_final: 0.7674 (tpt) REVERT: D 246 TYR cc_start: 0.9038 (t80) cc_final: 0.8786 (t80) REVERT: D 273 GLN cc_start: 0.8199 (tp40) cc_final: 0.7728 (tp40) REVERT: D 293 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 315 LEU cc_start: 0.9227 (mt) cc_final: 0.8902 (tt) REVERT: D 360 PRO cc_start: 0.9232 (Cg_exo) cc_final: 0.9027 (Cg_endo) REVERT: D 716 MET cc_start: 0.4614 (mpt) cc_final: 0.3528 (tpp) REVERT: D 738 TYR cc_start: 0.8106 (m-10) cc_final: 0.7817 (m-10) REVERT: D 748 ASN cc_start: 0.9116 (t0) cc_final: 0.8789 (t0) REVERT: B 214 MET cc_start: 0.7900 (tpt) cc_final: 0.7592 (tpt) REVERT: B 246 TYR cc_start: 0.9025 (t80) cc_final: 0.8666 (t80) REVERT: B 293 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8386 (mm-30) REVERT: B 324 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8483 (ptpp) REVERT: B 383 ASP cc_start: 0.7831 (t0) cc_final: 0.7563 (t0) REVERT: B 505 SER cc_start: 0.8449 (p) cc_final: 0.8209 (m) REVERT: B 748 ASN cc_start: 0.9137 (t0) cc_final: 0.8845 (t0) REVERT: C 214 MET cc_start: 0.7581 (tpt) cc_final: 0.7355 (tpt) REVERT: C 246 TYR cc_start: 0.9077 (t80) cc_final: 0.8763 (t80) REVERT: C 293 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8407 (mm-30) outliers start: 28 outliers final: 21 residues processed: 420 average time/residue: 1.0644 time to fit residues: 507.3141 Evaluate side-chains 408 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 387 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 741 CYS 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 674 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS C 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17924 Z= 0.177 Angle : 0.624 16.404 24320 Z= 0.301 Chirality : 0.038 0.161 2728 Planarity : 0.004 0.045 2992 Dihedral : 4.832 27.472 2720 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.33 % Allowed : 23.62 % Favored : 75.05 % 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: 1.57 (0.19), residues: 2120 helix: 2.37 (0.14), residues: 1260 sheet: -0.68 (0.57), residues: 76 loop : -1.08 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 272 HIS 0.005 0.001 HIS B 378 PHE 0.025 0.001 PHE C 266 TYR 0.022 0.001 TYR B 374 ARG 0.012 0.001 ARG B 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 404 time to evaluate : 1.889 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 246 TYR cc_start: 0.9044 (t80) cc_final: 0.8727 (t80) REVERT: A 273 GLN cc_start: 0.8307 (tp40) cc_final: 0.7866 (tp40) REVERT: A 293 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8365 (mm-30) REVERT: A 315 LEU cc_start: 0.9242 (mt) cc_final: 0.8953 (tt) REVERT: A 324 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8160 (ptpp) REVERT: A 327 GLU cc_start: 0.7687 (pp20) cc_final: 0.7125 (pp20) REVERT: A 420 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.8063 (mmm-85) REVERT: A 460 LEU cc_start: 0.8516 (mm) cc_final: 0.8181 (mt) REVERT: A 471 ASP cc_start: 0.8254 (m-30) cc_final: 0.7834 (t0) REVERT: D 214 MET cc_start: 0.7900 (tpt) cc_final: 0.7594 (tpt) REVERT: D 246 TYR cc_start: 0.9054 (t80) cc_final: 0.8794 (t80) REVERT: D 273 GLN cc_start: 0.8171 (tp40) cc_final: 0.7660 (tp40) REVERT: D 293 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8404 (mm-30) REVERT: D 315 LEU cc_start: 0.9230 (mt) cc_final: 0.8885 (tt) REVERT: D 429 PHE cc_start: 0.7989 (t80) cc_final: 0.7764 (t80) REVERT: D 716 MET cc_start: 0.4571 (mpt) cc_final: 0.3547 (tpp) REVERT: D 738 TYR cc_start: 0.8044 (m-10) cc_final: 0.7752 (m-10) REVERT: D 748 ASN cc_start: 0.9118 (t0) cc_final: 0.8800 (t0) REVERT: B 246 TYR cc_start: 0.9022 (t80) cc_final: 0.8683 (t80) REVERT: B 293 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 324 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8537 (ptpp) REVERT: B 383 ASP cc_start: 0.7842 (t0) cc_final: 0.7538 (t0) REVERT: B 505 SER cc_start: 0.8458 (p) cc_final: 0.8242 (m) REVERT: B 748 ASN cc_start: 0.9144 (t0) cc_final: 0.8849 (t0) REVERT: C 246 TYR cc_start: 0.9063 (t80) cc_final: 0.8771 (t80) REVERT: C 293 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8411 (mm-30) outliers start: 25 outliers final: 20 residues processed: 412 average time/residue: 1.0278 time to fit residues: 482.6552 Evaluate side-chains 403 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 383 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 168 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 172 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 147 optimal weight: 0.0370 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092434 restraints weight = 25592.906| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.32 r_work: 0.2856 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17924 Z= 0.147 Angle : 0.619 16.385 24320 Z= 0.296 Chirality : 0.038 0.162 2728 Planarity : 0.004 0.045 2992 Dihedral : 4.461 25.116 2720 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.49 % Allowed : 23.51 % Favored : 75.00 % 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: 1.65 (0.19), residues: 2120 helix: 2.44 (0.14), residues: 1256 sheet: -0.55 (0.59), residues: 76 loop : -1.04 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 272 HIS 0.003 0.001 HIS C 206 PHE 0.016 0.001 PHE A 429 TYR 0.014 0.001 TYR A 584 ARG 0.014 0.001 ARG D 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8346.28 seconds wall clock time: 147 minutes 8.59 seconds (8828.59 seconds total)