Starting phenix.real_space_refine on Sun Mar 17 09:26:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzc_24089/03_2024/7mzc_24089_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzc_24089/03_2024/7mzc_24089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzc_24089/03_2024/7mzc_24089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzc_24089/03_2024/7mzc_24089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzc_24089/03_2024/7mzc_24089_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mzc_24089/03_2024/7mzc_24089_updated.pdb" } resolution = 3.03 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 11384 2.51 5 N 2780 2.21 5 O 3068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 210": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "C ASP 654": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17334 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "D" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "B" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} Chain: "C" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4287 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 513} 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} Time building chain proxies: 9.33, per 1000 atoms: 0.54 Number of scatterers: 17334 At special positions: 0 Unit cell: (125.934, 125.934, 108.42, 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 3068 8.00 N 2780 7.00 C 11384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.1 seconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 4 sheets defined 59.2% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.235A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.126A 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: 4.046A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 3.731A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 598 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.860A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 673 through 711 removed outlier: 5.360A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 5.239A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.111A 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: 4.039A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 598 removed outlier: 4.597A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.005A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 673 through 711 removed outlier: 5.196A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 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 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 453 removed outlier: 5.231A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.067A 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: 4.036A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 574 removed outlier: 3.720A pdb=" N ALA B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 598 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.872A 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 670 Processing helix chain 'B' and resid 673 through 711 removed outlier: 5.550A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 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 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 453 removed outlier: 5.225A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.129A 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: 4.056A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 574 removed outlier: 3.821A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 598 Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.015A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 673 through 711 removed outlier: 5.240A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.855A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.931A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.635A 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: 3.836A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.819A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2685 1.31 - 1.44: 5067 1.44 - 1.57: 9836 1.57 - 1.70: 16 1.70 - 1.83: 164 Bond restraints: 17768 Sorted by residual: bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.182 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.183 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.184 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.184 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" CAV 6EU B 901 " pdb=" CBB 6EU B 901 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.34e+01 ... (remaining 17763 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.94: 232 104.94 - 112.24: 8808 112.24 - 119.53: 6154 119.53 - 126.82: 8727 126.82 - 134.12: 191 Bond angle restraints: 24112 Sorted by residual: angle pdb=" N ASP C 654 " pdb=" CA ASP C 654 " pdb=" C ASP C 654 " ideal model delta sigma weight residual 109.85 100.05 9.80 1.58e+00 4.01e-01 3.85e+01 angle pdb=" N ILE D 387 " pdb=" CA ILE D 387 " pdb=" C ILE D 387 " ideal model delta sigma weight residual 111.48 106.34 5.14 9.40e-01 1.13e+00 2.99e+01 angle pdb=" N SER C 722 " pdb=" CA SER C 722 " pdb=" CB SER C 722 " ideal model delta sigma weight residual 114.17 108.89 5.28 1.14e+00 7.69e-01 2.14e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 angle pdb=" N SER B 722 " pdb=" CA SER B 722 " pdb=" CB SER B 722 " ideal model delta sigma weight residual 114.17 109.02 5.15 1.14e+00 7.69e-01 2.04e+01 ... (remaining 24107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10097 17.78 - 35.55: 482 35.55 - 53.33: 89 53.33 - 71.11: 34 71.11 - 88.88: 17 Dihedral angle restraints: 10719 sinusoidal: 4499 harmonic: 6220 Sorted by residual: dihedral pdb=" CA PHE A 429 " pdb=" C PHE A 429 " pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta harmonic sigma weight residual 180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PHE B 429 " pdb=" C PHE B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta harmonic sigma weight residual -180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA PHE C 429 " pdb=" C PHE C 429 " pdb=" N VAL C 430 " pdb=" CA VAL C 430 " ideal model delta harmonic sigma weight residual -180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 10716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2649 0.105 - 0.209: 51 0.209 - 0.313: 4 0.313 - 0.418: 0 0.418 - 0.522: 12 Chirality restraints: 2716 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 2.13 0.52 2.00e-01 2.50e+01 6.82e+00 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 2.14 0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CAJ 6EU D 901 " pdb=" CAK 6EU D 901 " pdb=" CAN 6EU D 901 " pdb=" CAO 6EU D 901 " both_signs ideal model delta sigma weight residual False 2.66 2.14 0.51 2.00e-01 2.50e+01 6.55e+00 ... (remaining 2713 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " -0.110 2.00e-02 2.50e+03 1.91e-01 3.64e+02 pdb=" CAV 6EU D 901 " 0.331 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " -0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " -0.109 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" CAV 6EU C 901 " 0.330 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " -0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " 0.109 2.00e-02 2.50e+03 1.90e-01 3.59e+02 pdb=" CAV 6EU B 901 " -0.328 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " 0.110 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " 0.110 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 147 2.60 - 3.18: 15861 3.18 - 3.75: 26818 3.75 - 4.33: 38155 4.33 - 4.90: 62419 Nonbonded interactions: 143400 Sorted by model distance: nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.028 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.049 2.440 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.062 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.077 2.440 nonbonded pdb=" O GLY B 643 " pdb="NA NA A 902 " model vdw 2.334 2.470 ... (remaining 143395 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 202 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.160 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 48.210 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.012 0.240 17768 Z= 0.721 Angle : 0.905 13.521 24112 Z= 0.456 Chirality : 0.053 0.522 2716 Planarity : 0.008 0.191 2968 Dihedral : 12.070 88.883 6716 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 1.61 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2104 helix: 1.22 (0.14), residues: 1360 sheet: -1.03 (0.53), residues: 76 loop : -1.58 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 549 HIS 0.003 0.001 HIS B 206 PHE 0.029 0.002 PHE D 649 TYR 0.020 0.002 TYR D 627 ARG 0.005 0.001 ARG D 739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 714 time to evaluate : 1.971 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 273 GLN cc_start: 0.8014 (tp40) cc_final: 0.7771 (tp40) REVERT: A 315 LEU cc_start: 0.9019 (mt) cc_final: 0.8708 (mp) REVERT: A 368 LYS cc_start: 0.8170 (tttt) cc_final: 0.7876 (tttm) REVERT: A 369 PHE cc_start: 0.8744 (m-80) cc_final: 0.8448 (m-80) REVERT: A 385 SER cc_start: 0.8888 (t) cc_final: 0.8482 (m) REVERT: A 401 TYR cc_start: 0.8427 (m-80) cc_final: 0.8168 (m-10) REVERT: A 428 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7595 (mtt90) REVERT: A 435 TYR cc_start: 0.9056 (m-80) cc_final: 0.8828 (m-10) REVERT: A 438 PHE cc_start: 0.9224 (t80) cc_final: 0.8800 (t80) REVERT: A 465 LEU cc_start: 0.8864 (tp) cc_final: 0.8495 (tt) REVERT: A 478 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 513 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 561 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: A 737 ASP cc_start: 0.7391 (p0) cc_final: 0.7138 (p0) REVERT: A 745 ASP cc_start: 0.7609 (m-30) cc_final: 0.7249 (t0) REVERT: D 273 GLN cc_start: 0.7983 (tp40) cc_final: 0.7740 (tp40) REVERT: D 310 ASN cc_start: 0.8909 (t0) cc_final: 0.8519 (t0) REVERT: D 311 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8353 (mm-30) REVERT: D 315 LEU cc_start: 0.9058 (mt) cc_final: 0.8702 (mp) REVERT: D 368 LYS cc_start: 0.8277 (tttt) cc_final: 0.7630 (tttm) REVERT: D 378 HIS cc_start: 0.7865 (p-80) cc_final: 0.6918 (p-80) REVERT: D 385 SER cc_start: 0.8754 (t) cc_final: 0.8309 (m) REVERT: D 401 TYR cc_start: 0.8450 (m-80) cc_final: 0.8222 (m-10) REVERT: D 428 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7627 (mtt90) REVERT: D 438 PHE cc_start: 0.9242 (t80) cc_final: 0.8826 (t80) REVERT: D 465 LEU cc_start: 0.8878 (tp) cc_final: 0.8468 (tt) REVERT: D 561 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: B 266 PHE cc_start: 0.8745 (t80) cc_final: 0.8513 (t80) REVERT: B 310 ASN cc_start: 0.8882 (t0) cc_final: 0.8432 (t0) REVERT: B 311 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 315 LEU cc_start: 0.9058 (mt) cc_final: 0.8739 (mp) REVERT: B 378 HIS cc_start: 0.7790 (p-80) cc_final: 0.6522 (p-80) REVERT: B 385 SER cc_start: 0.8970 (t) cc_final: 0.8551 (m) REVERT: B 401 TYR cc_start: 0.8470 (m-80) cc_final: 0.8131 (m-10) REVERT: B 423 GLN cc_start: 0.8530 (tp40) cc_final: 0.8030 (tp-100) REVERT: B 428 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7670 (mtt90) REVERT: B 435 TYR cc_start: 0.9063 (m-80) cc_final: 0.8849 (m-10) REVERT: B 438 PHE cc_start: 0.9232 (t80) cc_final: 0.8819 (t80) REVERT: B 465 LEU cc_start: 0.8865 (tp) cc_final: 0.7973 (tp) REVERT: B 513 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8638 (mm-30) REVERT: B 561 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: B 698 LYS cc_start: 0.9134 (mttm) cc_final: 0.8606 (mtmm) REVERT: B 733 ASP cc_start: 0.7498 (p0) cc_final: 0.7226 (p0) REVERT: B 737 ASP cc_start: 0.7081 (p0) cc_final: 0.6784 (p0) REVERT: B 745 ASP cc_start: 0.7781 (m-30) cc_final: 0.7317 (t0) REVERT: C 266 PHE cc_start: 0.8817 (t80) cc_final: 0.8612 (t80) REVERT: C 273 GLN cc_start: 0.7994 (tp40) cc_final: 0.7743 (tp40) REVERT: C 310 ASN cc_start: 0.8893 (t0) cc_final: 0.8587 (t0) REVERT: C 315 LEU cc_start: 0.8984 (mt) cc_final: 0.8761 (mp) REVERT: C 369 PHE cc_start: 0.8636 (m-80) cc_final: 0.8285 (m-80) REVERT: C 378 HIS cc_start: 0.7760 (p-80) cc_final: 0.6829 (p-80) REVERT: C 385 SER cc_start: 0.9104 (t) cc_final: 0.8874 (t) REVERT: C 397 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 401 TYR cc_start: 0.8481 (m-80) cc_final: 0.8206 (m-10) REVERT: C 409 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.7932 (ttp-170) REVERT: C 428 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7615 (mtt90) REVERT: C 438 PHE cc_start: 0.9237 (t80) cc_final: 0.8823 (t80) REVERT: C 465 LEU cc_start: 0.8862 (tp) cc_final: 0.8458 (tt) REVERT: C 478 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8193 (mt-10) REVERT: C 504 LYS cc_start: 0.8866 (mttt) cc_final: 0.8616 (mptt) REVERT: C 506 LEU cc_start: 0.9002 (tp) cc_final: 0.8772 (tp) REVERT: C 513 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8411 (mm-30) REVERT: C 561 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: C 733 ASP cc_start: 0.7553 (p0) cc_final: 0.7350 (p0) REVERT: C 737 ASP cc_start: 0.7409 (p0) cc_final: 0.7201 (p0) REVERT: C 745 ASP cc_start: 0.7695 (m-30) cc_final: 0.7227 (t0) outliers start: 21 outliers final: 2 residues processed: 719 average time/residue: 0.3350 time to fit residues: 339.8394 Evaluate side-chains 465 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 459 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 561 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 301 ASN A 393 ASN A 652 ASN D 310 ASN D 561 GLN D 652 ASN B 310 ASN B 354 GLN B 358 HIS B 652 ASN B 676 ASN B 727 GLN C 652 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17768 Z= 0.222 Angle : 0.538 7.178 24112 Z= 0.289 Chirality : 0.039 0.133 2716 Planarity : 0.004 0.069 2968 Dihedral : 8.322 75.893 2714 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.39 % Rotamer: Outliers : 1.66 % Allowed : 10.92 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2104 helix: 1.64 (0.14), residues: 1328 sheet: -0.24 (0.57), residues: 76 loop : -1.48 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 697 HIS 0.005 0.001 HIS B 358 PHE 0.031 0.001 PHE A 304 TYR 0.015 0.002 TYR D 401 ARG 0.006 0.001 ARG D 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 529 time to evaluate : 2.136 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 260 GLN cc_start: 0.8499 (mt0) cc_final: 0.8246 (mt0) REVERT: A 325 LEU cc_start: 0.9254 (mt) cc_final: 0.8909 (mt) REVERT: A 351 TYR cc_start: 0.8742 (t80) cc_final: 0.8468 (t80) REVERT: A 369 PHE cc_start: 0.8392 (m-80) cc_final: 0.8072 (m-10) REVERT: A 383 ASP cc_start: 0.7779 (t0) cc_final: 0.7412 (t0) REVERT: A 385 SER cc_start: 0.8769 (t) cc_final: 0.8165 (m) REVERT: A 394 SER cc_start: 0.8951 (m) cc_final: 0.8398 (p) REVERT: A 401 TYR cc_start: 0.8531 (m-80) cc_final: 0.8176 (m-10) REVERT: A 423 GLN cc_start: 0.8464 (tp40) cc_final: 0.8223 (tp-100) REVERT: A 424 ASP cc_start: 0.8762 (t70) cc_final: 0.8368 (t70) REVERT: A 428 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7725 (mtt90) REVERT: A 435 TYR cc_start: 0.9079 (m-80) cc_final: 0.8823 (m-10) REVERT: A 438 PHE cc_start: 0.9233 (t80) cc_final: 0.8797 (t80) REVERT: A 561 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: D 309 TYR cc_start: 0.9187 (t80) cc_final: 0.8975 (t80) REVERT: D 325 LEU cc_start: 0.9232 (mt) cc_final: 0.8977 (mt) REVERT: D 385 SER cc_start: 0.8700 (t) cc_final: 0.8108 (m) REVERT: D 394 SER cc_start: 0.8909 (m) cc_final: 0.8606 (p) REVERT: D 397 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7530 (mt-10) REVERT: D 428 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7769 (mtt90) REVERT: D 438 PHE cc_start: 0.9239 (t80) cc_final: 0.8820 (t80) REVERT: D 561 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: D 724 LYS cc_start: 0.8401 (tptm) cc_final: 0.8090 (tptm) REVERT: B 325 LEU cc_start: 0.9205 (mt) cc_final: 0.8953 (mt) REVERT: B 351 TYR cc_start: 0.8858 (t80) cc_final: 0.8605 (t80) REVERT: B 383 ASP cc_start: 0.7729 (t0) cc_final: 0.7305 (t0) REVERT: B 385 SER cc_start: 0.8771 (t) cc_final: 0.8237 (m) REVERT: B 394 SER cc_start: 0.9028 (m) cc_final: 0.8396 (p) REVERT: B 397 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7326 (mt-10) REVERT: B 438 PHE cc_start: 0.9229 (t80) cc_final: 0.8801 (t80) REVERT: B 513 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8584 (mm-30) REVERT: B 561 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: C 325 LEU cc_start: 0.9197 (mt) cc_final: 0.8924 (mt) REVERT: C 383 ASP cc_start: 0.7731 (t0) cc_final: 0.7321 (t0) REVERT: C 385 SER cc_start: 0.9051 (t) cc_final: 0.8329 (m) REVERT: C 397 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 409 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.8030 (ttp-170) REVERT: C 424 ASP cc_start: 0.8655 (t70) cc_final: 0.8375 (t70) REVERT: C 428 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7727 (mtt90) REVERT: C 438 PHE cc_start: 0.9255 (t80) cc_final: 0.8777 (t80) REVERT: C 504 LYS cc_start: 0.8872 (mttt) cc_final: 0.8616 (mptt) REVERT: C 513 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8391 (mm-30) REVERT: C 561 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8211 (pm20) outliers start: 31 outliers final: 15 residues processed: 541 average time/residue: 0.2893 time to fit residues: 231.8954 Evaluate side-chains 490 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 471 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 561 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 168 optimal weight: 0.0040 chunk 187 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN B 206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17768 Z= 0.209 Angle : 0.521 7.400 24112 Z= 0.278 Chirality : 0.039 0.135 2716 Planarity : 0.004 0.049 2968 Dihedral : 7.806 83.921 2711 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 1.71 % Allowed : 13.87 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2104 helix: 1.73 (0.14), residues: 1328 sheet: 0.02 (0.57), residues: 76 loop : -1.54 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 372 HIS 0.004 0.001 HIS B 206 PHE 0.022 0.001 PHE A 304 TYR 0.013 0.001 TYR C 511 ARG 0.007 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 517 time to evaluate : 1.697 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 351 TYR cc_start: 0.8789 (t80) cc_final: 0.8392 (t80) REVERT: A 369 PHE cc_start: 0.8410 (m-80) cc_final: 0.8067 (m-10) REVERT: A 394 SER cc_start: 0.8841 (m) cc_final: 0.8540 (t) REVERT: A 401 TYR cc_start: 0.8533 (m-80) cc_final: 0.8073 (m-10) REVERT: A 435 TYR cc_start: 0.9088 (m-80) cc_final: 0.8862 (m-10) REVERT: A 438 PHE cc_start: 0.9265 (t80) cc_final: 0.8968 (t80) REVERT: A 561 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: A 743 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8143 (ttm-80) REVERT: D 291 LEU cc_start: 0.9120 (mt) cc_final: 0.8811 (mt) REVERT: D 383 ASP cc_start: 0.7949 (t0) cc_final: 0.7666 (t0) REVERT: D 394 SER cc_start: 0.8940 (m) cc_final: 0.8500 (p) REVERT: D 397 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 438 PHE cc_start: 0.9271 (t80) cc_final: 0.8796 (t80) REVERT: D 561 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: B 351 TYR cc_start: 0.8922 (t80) cc_final: 0.8550 (t80) REVERT: B 383 ASP cc_start: 0.7698 (t0) cc_final: 0.7301 (t0) REVERT: B 385 SER cc_start: 0.8720 (t) cc_final: 0.8135 (m) REVERT: B 394 SER cc_start: 0.8974 (m) cc_final: 0.8466 (p) REVERT: B 397 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 438 PHE cc_start: 0.9265 (t80) cc_final: 0.8785 (t80) REVERT: B 513 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8596 (mm-30) REVERT: B 561 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: C 383 ASP cc_start: 0.7706 (t0) cc_final: 0.7327 (t0) REVERT: C 385 SER cc_start: 0.9007 (t) cc_final: 0.8314 (m) REVERT: C 397 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 401 TYR cc_start: 0.8550 (m-80) cc_final: 0.8296 (m-10) REVERT: C 409 ARG cc_start: 0.8402 (ptm-80) cc_final: 0.7949 (ttp-170) REVERT: C 428 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7722 (mtt90) REVERT: C 438 PHE cc_start: 0.9251 (t80) cc_final: 0.8976 (t80) REVERT: C 472 TYR cc_start: 0.8653 (m-80) cc_final: 0.8404 (m-10) REVERT: C 504 LYS cc_start: 0.8820 (mttt) cc_final: 0.8564 (mptt) REVERT: C 513 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8526 (mm-30) REVERT: C 561 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: C 743 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7966 (ttm-80) outliers start: 32 outliers final: 16 residues processed: 530 average time/residue: 0.2804 time to fit residues: 222.5241 Evaluate side-chains 507 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 487 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 561 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN B 727 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17768 Z= 0.166 Angle : 0.501 12.395 24112 Z= 0.266 Chirality : 0.037 0.140 2716 Planarity : 0.004 0.048 2968 Dihedral : 7.314 89.295 2711 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 1.87 % Allowed : 14.40 % Favored : 83.73 % 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: 1.14 (0.19), residues: 2104 helix: 1.91 (0.14), residues: 1300 sheet: 0.19 (0.58), residues: 76 loop : -1.37 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 372 HIS 0.002 0.001 HIS D 378 PHE 0.023 0.001 PHE A 304 TYR 0.013 0.001 TYR C 511 ARG 0.004 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 516 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8744 (t80) cc_final: 0.8320 (t80) REVERT: A 369 PHE cc_start: 0.8314 (m-80) cc_final: 0.8062 (m-10) REVERT: A 374 TYR cc_start: 0.7784 (t80) cc_final: 0.7488 (t80) REVERT: A 394 SER cc_start: 0.8757 (m) cc_final: 0.8518 (t) REVERT: A 401 TYR cc_start: 0.8556 (m-80) cc_final: 0.8046 (m-10) REVERT: A 438 PHE cc_start: 0.9254 (t80) cc_final: 0.8790 (t80) REVERT: A 560 GLN cc_start: 0.8564 (tp40) cc_final: 0.8290 (tp40) REVERT: A 561 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: A 564 ILE cc_start: 0.8215 (mt) cc_final: 0.7877 (mt) REVERT: A 743 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8163 (ttm-80) REVERT: D 291 LEU cc_start: 0.9120 (mt) cc_final: 0.8802 (mp) REVERT: D 351 TYR cc_start: 0.8926 (t80) cc_final: 0.8613 (t80) REVERT: D 438 PHE cc_start: 0.9259 (t80) cc_final: 0.8762 (t80) REVERT: D 561 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: B 351 TYR cc_start: 0.8886 (t80) cc_final: 0.8541 (t80) REVERT: B 383 ASP cc_start: 0.7606 (t0) cc_final: 0.7360 (t0) REVERT: B 385 SER cc_start: 0.8690 (t) cc_final: 0.8271 (m) REVERT: B 394 SER cc_start: 0.8964 (m) cc_final: 0.8442 (p) REVERT: B 397 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7244 (mt-10) REVERT: B 438 PHE cc_start: 0.9249 (t80) cc_final: 0.8747 (t80) REVERT: B 513 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8572 (mm-30) REVERT: B 561 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: B 564 ILE cc_start: 0.8164 (mt) cc_final: 0.7822 (mt) REVERT: C 397 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 438 PHE cc_start: 0.9252 (t80) cc_final: 0.8785 (t80) REVERT: C 472 TYR cc_start: 0.8614 (m-80) cc_final: 0.8394 (m-10) REVERT: C 504 LYS cc_start: 0.8798 (mttt) cc_final: 0.8506 (mptt) REVERT: C 561 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: C 743 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8033 (ttm-80) outliers start: 35 outliers final: 25 residues processed: 532 average time/residue: 0.2795 time to fit residues: 223.9534 Evaluate side-chains 490 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 461 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 576 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN D 419 ASN C 410 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17768 Z= 0.174 Angle : 0.505 8.041 24112 Z= 0.268 Chirality : 0.038 0.144 2716 Planarity : 0.004 0.048 2968 Dihedral : 6.896 89.553 2711 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.46 % Allowed : 15.47 % Favored : 82.07 % 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: 1.14 (0.19), residues: 2104 helix: 1.92 (0.14), residues: 1300 sheet: 0.30 (0.59), residues: 76 loop : -1.40 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 372 HIS 0.002 0.001 HIS A 289 PHE 0.019 0.001 PHE A 304 TYR 0.013 0.001 TYR C 511 ARG 0.007 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 472 time to evaluate : 1.814 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 351 TYR cc_start: 0.8777 (t80) cc_final: 0.8378 (t80) REVERT: A 369 PHE cc_start: 0.8286 (m-80) cc_final: 0.8030 (m-80) REVERT: A 384 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 394 SER cc_start: 0.8809 (m) cc_final: 0.8521 (t) REVERT: A 401 TYR cc_start: 0.8600 (m-80) cc_final: 0.8032 (m-10) REVERT: A 409 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8290 (ttt180) REVERT: A 438 PHE cc_start: 0.9262 (t80) cc_final: 0.8793 (t80) REVERT: A 561 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: A 564 ILE cc_start: 0.8300 (mt) cc_final: 0.7978 (mt) REVERT: A 743 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: D 291 LEU cc_start: 0.9111 (mt) cc_final: 0.8778 (mp) REVERT: D 308 MET cc_start: 0.8979 (tpp) cc_final: 0.8724 (tpp) REVERT: D 310 ASN cc_start: 0.8468 (t0) cc_final: 0.8250 (t0) REVERT: D 351 TYR cc_start: 0.8892 (t80) cc_final: 0.8573 (t80) REVERT: D 381 LEU cc_start: 0.7746 (mm) cc_final: 0.7368 (mt) REVERT: D 394 SER cc_start: 0.8929 (m) cc_final: 0.8517 (p) REVERT: D 397 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7616 (pt0) REVERT: D 438 PHE cc_start: 0.9264 (t80) cc_final: 0.8755 (t80) REVERT: D 561 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: B 308 MET cc_start: 0.8960 (tpp) cc_final: 0.8662 (tpp) REVERT: B 310 ASN cc_start: 0.8425 (t0) cc_final: 0.8197 (t0) REVERT: B 351 TYR cc_start: 0.8889 (t80) cc_final: 0.8504 (t80) REVERT: B 438 PHE cc_start: 0.9252 (t80) cc_final: 0.8754 (t80) REVERT: B 491 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: B 561 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: B 564 ILE cc_start: 0.8286 (mt) cc_final: 0.7956 (mt) REVERT: C 351 TYR cc_start: 0.8853 (t80) cc_final: 0.8391 (t80) REVERT: C 383 ASP cc_start: 0.7637 (t0) cc_final: 0.7302 (t0) REVERT: C 385 SER cc_start: 0.8863 (t) cc_final: 0.8293 (m) REVERT: C 397 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7740 (mt-10) REVERT: C 438 PHE cc_start: 0.9259 (t80) cc_final: 0.8797 (t80) REVERT: C 472 TYR cc_start: 0.8614 (m-80) cc_final: 0.8403 (m-10) REVERT: C 504 LYS cc_start: 0.8815 (mttt) cc_final: 0.8529 (mptt) REVERT: C 560 GLN cc_start: 0.8622 (tt0) cc_final: 0.8372 (tt0) REVERT: C 564 ILE cc_start: 0.8278 (mt) cc_final: 0.7927 (mt) REVERT: C 743 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8080 (ttm-80) outliers start: 46 outliers final: 29 residues processed: 494 average time/residue: 0.3037 time to fit residues: 225.1569 Evaluate side-chains 481 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 448 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 576 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 ASN D 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17768 Z= 0.252 Angle : 0.535 8.422 24112 Z= 0.284 Chirality : 0.039 0.164 2716 Planarity : 0.004 0.049 2968 Dihedral : 6.542 83.709 2705 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.52 % Allowed : 15.74 % Favored : 81.75 % 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: 1.04 (0.19), residues: 2104 helix: 1.83 (0.14), residues: 1300 sheet: -0.04 (0.60), residues: 76 loop : -1.40 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 372 HIS 0.002 0.001 HIS D 289 PHE 0.020 0.001 PHE A 304 TYR 0.012 0.001 TYR C 511 ARG 0.007 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 452 time to evaluate : 2.006 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 351 TYR cc_start: 0.8811 (t80) cc_final: 0.8382 (t80) REVERT: A 384 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 401 TYR cc_start: 0.8624 (m-80) cc_final: 0.7971 (m-10) REVERT: A 409 ARG cc_start: 0.8570 (ttt180) cc_final: 0.8279 (ttt180) REVERT: A 438 PHE cc_start: 0.9259 (t80) cc_final: 0.8975 (t80) REVERT: A 564 ILE cc_start: 0.8420 (mt) cc_final: 0.8138 (mt) REVERT: D 291 LEU cc_start: 0.9131 (mt) cc_final: 0.8792 (mp) REVERT: D 308 MET cc_start: 0.8966 (tpp) cc_final: 0.8724 (tpp) REVERT: D 310 ASN cc_start: 0.8451 (t0) cc_final: 0.8213 (t0) REVERT: D 351 TYR cc_start: 0.8941 (t80) cc_final: 0.8592 (t80) REVERT: D 397 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7666 (pt0) REVERT: D 438 PHE cc_start: 0.9266 (t80) cc_final: 0.8992 (t80) REVERT: D 561 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: D 694 LYS cc_start: 0.8328 (pttt) cc_final: 0.8016 (pttm) REVERT: B 308 MET cc_start: 0.8969 (tpp) cc_final: 0.8693 (tpp) REVERT: B 310 ASN cc_start: 0.8453 (t0) cc_final: 0.8208 (t0) REVERT: B 351 TYR cc_start: 0.8890 (t80) cc_final: 0.8470 (t80) REVERT: B 397 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7812 (pt0) REVERT: B 564 ILE cc_start: 0.8389 (mt) cc_final: 0.8076 (mt) REVERT: C 385 SER cc_start: 0.8875 (t) cc_final: 0.8464 (m) REVERT: C 401 TYR cc_start: 0.8585 (m-10) cc_final: 0.8021 (m-10) REVERT: C 438 PHE cc_start: 0.9255 (t80) cc_final: 0.8776 (t80) REVERT: C 472 TYR cc_start: 0.8624 (m-80) cc_final: 0.8390 (m-10) REVERT: C 504 LYS cc_start: 0.8813 (mttt) cc_final: 0.8544 (mptt) REVERT: C 564 ILE cc_start: 0.8438 (mt) cc_final: 0.8126 (mt) REVERT: C 743 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8157 (ttm-80) outliers start: 47 outliers final: 36 residues processed: 470 average time/residue: 0.2884 time to fit residues: 202.5078 Evaluate side-chains 475 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 437 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 125 optimal weight: 0.0050 chunk 122 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17768 Z= 0.194 Angle : 0.537 14.369 24112 Z= 0.280 Chirality : 0.039 0.143 2716 Planarity : 0.004 0.048 2968 Dihedral : 5.823 79.950 2699 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.73 % Allowed : 16.54 % Favored : 80.73 % 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: 1.00 (0.19), residues: 2104 helix: 1.80 (0.14), residues: 1300 sheet: -0.28 (0.60), residues: 76 loop : -1.39 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 372 HIS 0.003 0.001 HIS C 206 PHE 0.019 0.001 PHE A 304 TYR 0.013 0.001 TYR C 511 ARG 0.008 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 455 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8756 (t80) cc_final: 0.8325 (t80) REVERT: A 394 SER cc_start: 0.8824 (m) cc_final: 0.8510 (p) REVERT: A 401 TYR cc_start: 0.8621 (m-80) cc_final: 0.7846 (m-10) REVERT: A 409 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8251 (ttt180) REVERT: A 438 PHE cc_start: 0.9257 (t80) cc_final: 0.8770 (t80) REVERT: A 564 ILE cc_start: 0.8416 (mt) cc_final: 0.8139 (mt) REVERT: D 291 LEU cc_start: 0.9099 (mt) cc_final: 0.8758 (mp) REVERT: D 308 MET cc_start: 0.8957 (tpp) cc_final: 0.8725 (tpp) REVERT: D 309 TYR cc_start: 0.9225 (t80) cc_final: 0.8785 (t80) REVERT: D 310 ASN cc_start: 0.8490 (t0) cc_final: 0.8222 (t0) REVERT: D 351 TYR cc_start: 0.8920 (t80) cc_final: 0.8496 (t80) REVERT: D 397 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7692 (pt0) REVERT: D 438 PHE cc_start: 0.9250 (t80) cc_final: 0.8791 (t80) REVERT: D 561 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: B 308 MET cc_start: 0.8992 (tpp) cc_final: 0.8687 (tpp) REVERT: B 310 ASN cc_start: 0.8449 (t0) cc_final: 0.8199 (t0) REVERT: B 351 TYR cc_start: 0.8885 (t80) cc_final: 0.8403 (t80) REVERT: B 438 PHE cc_start: 0.9252 (t80) cc_final: 0.8784 (t80) REVERT: B 564 ILE cc_start: 0.8412 (mt) cc_final: 0.8131 (mt) REVERT: C 383 ASP cc_start: 0.7717 (t0) cc_final: 0.7400 (t0) REVERT: C 385 SER cc_start: 0.8790 (t) cc_final: 0.8256 (m) REVERT: C 401 TYR cc_start: 0.8598 (m-10) cc_final: 0.7647 (m-10) REVERT: C 409 ARG cc_start: 0.8685 (ptm160) cc_final: 0.7979 (ttp-170) REVERT: C 438 PHE cc_start: 0.9240 (t80) cc_final: 0.8769 (t80) REVERT: C 472 TYR cc_start: 0.8618 (m-80) cc_final: 0.8367 (m-10) REVERT: C 504 LYS cc_start: 0.8808 (mttt) cc_final: 0.8542 (mptt) REVERT: C 561 GLN cc_start: 0.8982 (mp10) cc_final: 0.8097 (pm20) REVERT: C 564 ILE cc_start: 0.8420 (mt) cc_final: 0.8115 (mt) outliers start: 51 outliers final: 43 residues processed: 476 average time/residue: 0.2831 time to fit residues: 202.0855 Evaluate side-chains 486 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 442 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 697 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 0.0000 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17768 Z= 0.180 Angle : 0.542 15.040 24112 Z= 0.281 Chirality : 0.039 0.182 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.478 75.713 2699 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.36 % Allowed : 17.18 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 2104 helix: 1.84 (0.14), residues: 1296 sheet: -0.34 (0.61), residues: 76 loop : -1.42 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 372 HIS 0.002 0.001 HIS B 289 PHE 0.019 0.001 PHE A 304 TYR 0.024 0.001 TYR A 309 ARG 0.008 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 459 time to evaluate : 2.054 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 310 ASN cc_start: 0.8370 (t0) cc_final: 0.8125 (t0) REVERT: A 351 TYR cc_start: 0.8729 (t80) cc_final: 0.8328 (t80) REVERT: A 384 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 394 SER cc_start: 0.8792 (m) cc_final: 0.8508 (p) REVERT: A 401 TYR cc_start: 0.8623 (m-80) cc_final: 0.7650 (m-10) REVERT: A 409 ARG cc_start: 0.8553 (ttt180) cc_final: 0.8266 (ttt180) REVERT: A 438 PHE cc_start: 0.9245 (t80) cc_final: 0.8773 (t80) REVERT: A 491 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.7860 (mmm-85) REVERT: A 564 ILE cc_start: 0.8419 (mt) cc_final: 0.8150 (mt) REVERT: D 291 LEU cc_start: 0.9075 (mt) cc_final: 0.8732 (mp) REVERT: D 308 MET cc_start: 0.8931 (tpp) cc_final: 0.8714 (tpp) REVERT: D 309 TYR cc_start: 0.9208 (t80) cc_final: 0.8769 (t80) REVERT: D 310 ASN cc_start: 0.8497 (t0) cc_final: 0.8207 (t0) REVERT: D 351 TYR cc_start: 0.8882 (t80) cc_final: 0.8463 (t80) REVERT: D 397 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7715 (pt0) REVERT: D 438 PHE cc_start: 0.9260 (t80) cc_final: 0.8798 (t80) REVERT: D 561 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: B 266 PHE cc_start: 0.8866 (t80) cc_final: 0.8612 (t80) REVERT: B 308 MET cc_start: 0.8986 (tpp) cc_final: 0.8673 (tpp) REVERT: B 310 ASN cc_start: 0.8459 (t0) cc_final: 0.8172 (t0) REVERT: B 351 TYR cc_start: 0.8825 (t80) cc_final: 0.8492 (t80) REVERT: B 438 PHE cc_start: 0.9257 (t80) cc_final: 0.8790 (t80) REVERT: B 564 ILE cc_start: 0.8395 (mt) cc_final: 0.8122 (mt) REVERT: C 351 TYR cc_start: 0.8894 (t80) cc_final: 0.8648 (t80) REVERT: C 383 ASP cc_start: 0.7690 (t0) cc_final: 0.7415 (t0) REVERT: C 385 SER cc_start: 0.8753 (t) cc_final: 0.8201 (m) REVERT: C 401 TYR cc_start: 0.8640 (m-10) cc_final: 0.7493 (m-10) REVERT: C 409 ARG cc_start: 0.8716 (ptm160) cc_final: 0.8289 (ptm160) REVERT: C 428 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7749 (mtt90) REVERT: C 438 PHE cc_start: 0.9247 (t80) cc_final: 0.8774 (t80) REVERT: C 472 TYR cc_start: 0.8622 (m-80) cc_final: 0.8385 (m-10) REVERT: C 504 LYS cc_start: 0.8838 (mttt) cc_final: 0.8572 (mptt) REVERT: C 564 ILE cc_start: 0.8445 (mt) cc_final: 0.8136 (mt) outliers start: 44 outliers final: 36 residues processed: 476 average time/residue: 0.2940 time to fit residues: 210.1174 Evaluate side-chains 487 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 449 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 576 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 0.0980 chunk 176 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN D 202 GLN C 408 ASN C 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17768 Z= 0.231 Angle : 0.575 16.233 24112 Z= 0.294 Chirality : 0.040 0.168 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.524 69.168 2699 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.68 % Allowed : 17.51 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 2104 helix: 1.79 (0.14), residues: 1300 sheet: -0.48 (0.61), residues: 76 loop : -1.39 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 372 HIS 0.003 0.001 HIS B 289 PHE 0.019 0.001 PHE A 304 TYR 0.014 0.001 TYR B 309 ARG 0.009 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 445 time to evaluate : 2.053 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 384 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 394 SER cc_start: 0.8782 (m) cc_final: 0.8515 (p) REVERT: A 409 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8264 (ttt180) REVERT: A 438 PHE cc_start: 0.9248 (t80) cc_final: 0.8964 (t80) REVERT: A 491 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.7849 (mmm-85) REVERT: A 564 ILE cc_start: 0.8439 (mt) cc_final: 0.8168 (mt) REVERT: D 291 LEU cc_start: 0.9095 (mt) cc_final: 0.8752 (mp) REVERT: D 351 TYR cc_start: 0.8932 (t80) cc_final: 0.8563 (t80) REVERT: D 385 SER cc_start: 0.8816 (t) cc_final: 0.8583 (t) REVERT: D 397 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7666 (pt0) REVERT: D 491 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.7861 (mmm-85) REVERT: D 561 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: B 308 MET cc_start: 0.8973 (tpp) cc_final: 0.8674 (tpp) REVERT: B 310 ASN cc_start: 0.8477 (t0) cc_final: 0.8189 (t0) REVERT: B 351 TYR cc_start: 0.8858 (t80) cc_final: 0.8512 (t80) REVERT: B 564 ILE cc_start: 0.8428 (mt) cc_final: 0.8156 (mt) REVERT: C 383 ASP cc_start: 0.7680 (t0) cc_final: 0.7412 (t0) REVERT: C 385 SER cc_start: 0.8794 (t) cc_final: 0.8235 (m) REVERT: C 401 TYR cc_start: 0.8683 (m-10) cc_final: 0.7448 (m-10) REVERT: C 409 ARG cc_start: 0.8710 (ptm160) cc_final: 0.8052 (ttp-170) REVERT: C 428 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7750 (mtt90) REVERT: C 472 TYR cc_start: 0.8638 (m-80) cc_final: 0.8381 (m-10) REVERT: C 504 LYS cc_start: 0.8863 (mttt) cc_final: 0.8591 (mptt) REVERT: C 564 ILE cc_start: 0.8441 (mt) cc_final: 0.8122 (mt) outliers start: 50 outliers final: 43 residues processed: 470 average time/residue: 0.2817 time to fit residues: 199.0248 Evaluate side-chains 487 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 442 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17768 Z= 0.185 Angle : 0.567 14.652 24112 Z= 0.290 Chirality : 0.039 0.211 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.290 65.056 2699 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.36 % Allowed : 17.93 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2104 helix: 1.81 (0.14), residues: 1296 sheet: -0.60 (0.61), residues: 76 loop : -1.44 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 372 HIS 0.002 0.001 HIS B 289 PHE 0.019 0.001 PHE A 304 TYR 0.014 0.001 TYR C 511 ARG 0.009 0.001 ARG C 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 453 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8760 (t80) cc_final: 0.8492 (t80) REVERT: A 384 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 394 SER cc_start: 0.8755 (m) cc_final: 0.8523 (p) REVERT: A 409 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8265 (ttt180) REVERT: A 438 PHE cc_start: 0.9252 (t80) cc_final: 0.8764 (t80) REVERT: A 443 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8983 (mp) REVERT: A 491 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.7842 (mmm-85) REVERT: A 564 ILE cc_start: 0.8421 (mt) cc_final: 0.8156 (mt) REVERT: D 291 LEU cc_start: 0.9039 (mt) cc_final: 0.8733 (mp) REVERT: D 310 ASN cc_start: 0.8480 (t0) cc_final: 0.8222 (t0) REVERT: D 351 TYR cc_start: 0.8872 (t80) cc_final: 0.8518 (t80) REVERT: D 361 GLU cc_start: 0.6759 (tp30) cc_final: 0.6557 (tp30) REVERT: D 385 SER cc_start: 0.8877 (t) cc_final: 0.8579 (t) REVERT: D 397 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7699 (pt0) REVERT: D 438 PHE cc_start: 0.9238 (t80) cc_final: 0.8785 (t80) REVERT: D 491 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.7840 (mmm-85) REVERT: D 561 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: B 308 MET cc_start: 0.8966 (tpp) cc_final: 0.8643 (tpp) REVERT: B 310 ASN cc_start: 0.8467 (t0) cc_final: 0.8153 (t0) REVERT: B 351 TYR cc_start: 0.8797 (t80) cc_final: 0.8529 (t80) REVERT: B 564 ILE cc_start: 0.8410 (mt) cc_final: 0.8138 (mt) REVERT: C 266 PHE cc_start: 0.8911 (t80) cc_final: 0.8654 (t80) REVERT: C 351 TYR cc_start: 0.8884 (t80) cc_final: 0.8671 (t80) REVERT: C 369 PHE cc_start: 0.7839 (m-80) cc_final: 0.7535 (m-80) REVERT: C 383 ASP cc_start: 0.7657 (t0) cc_final: 0.7395 (t0) REVERT: C 385 SER cc_start: 0.8769 (t) cc_final: 0.8220 (m) REVERT: C 401 TYR cc_start: 0.8690 (m-10) cc_final: 0.7443 (m-10) REVERT: C 409 ARG cc_start: 0.8720 (ptm160) cc_final: 0.8059 (ttp-170) REVERT: C 428 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7766 (mtt90) REVERT: C 438 PHE cc_start: 0.9237 (t80) cc_final: 0.8764 (t80) REVERT: C 472 TYR cc_start: 0.8623 (m-80) cc_final: 0.8388 (m-10) REVERT: C 491 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.7852 (mmm-85) REVERT: C 504 LYS cc_start: 0.8851 (mttt) cc_final: 0.8592 (mptt) REVERT: C 564 ILE cc_start: 0.8425 (mt) cc_final: 0.8109 (mt) outliers start: 44 outliers final: 35 residues processed: 475 average time/residue: 0.2757 time to fit residues: 197.7411 Evaluate side-chains 482 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 444 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095644 restraints weight = 25416.848| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.44 r_work: 0.2926 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17768 Z= 0.178 Angle : 0.571 14.837 24112 Z= 0.290 Chirality : 0.039 0.247 2716 Planarity : 0.004 0.049 2968 Dihedral : 5.054 60.306 2699 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.41 % Allowed : 18.09 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2104 helix: 1.83 (0.14), residues: 1296 sheet: -0.55 (0.62), residues: 76 loop : -1.42 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 372 HIS 0.003 0.001 HIS A 289 PHE 0.021 0.001 PHE A 304 TYR 0.014 0.001 TYR C 511 ARG 0.010 0.000 ARG C 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4913.55 seconds wall clock time: 88 minutes 10.92 seconds (5290.92 seconds total)