Starting phenix.real_space_refine on Sat Sep 12 16:50:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xt4_33439/09_2026/7xt4_33439.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 55 5.49 5 S 57 5.16 5 C 10507 2.51 5 N 2922 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16850 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5482 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain breaks: 1 Chain: "a" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 459 Classifications: {'RNAv2': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "B" Number of atoms: 10193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 10193 Classifications: {'peptide': 1263} Link IDs: {'PTRANS': 60, 'TRANS': 1202} Chain breaks: 7 Chain: "r" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 1, 'rna3p_pyr': 12} Link IDs: {'rna2p': 20, 'rna3p': 13} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6617 SG CYS B 88 69.236 51.264 18.108 1.00 41.87 S ATOM 6888 SG CYS B 121 72.218 50.046 16.186 1.00 51.33 S ATOM 6934 SG CYS B 127 71.610 54.386 17.267 1.00 42.32 S ATOM 6958 SG CYS B 130 72.514 51.521 19.618 1.00 38.21 S ATOM 9594 SG CYS B 491 49.232 60.089 44.134 1.00 39.36 S ATOM 9662 SG CYS B 501 49.685 57.275 41.816 1.00 39.98 S ATOM 9676 SG CYS B 503 47.626 60.653 40.826 1.00 37.90 S ATOM 9698 SG CYS B 506 51.196 61.705 41.537 1.00 34.99 S ATOM 11669 SG CYS B 750 36.047 67.390 71.264 1.00 54.75 S ATOM 11682 SG CYS B 752 34.161 70.734 70.109 1.00 48.11 S ATOM 11704 SG CYS B 755 37.980 70.862 69.011 1.00 44.09 S ATOM 13698 SG CYS B1018 39.285 93.746 98.661 1.00 43.47 S ATOM 13869 SG CYS B1406 39.618 90.193 97.791 1.00 45.00 S ATOM 13920 SG CYS B1414 36.084 92.177 97.473 1.00 40.04 S ATOM 13937 SG CYS B1417 38.290 92.828 94.530 1.00 36.98 S Time building chain proxies: 3.42, per 1000 atoms: 0.20 Number of scatterers: 16850 At special positions: 0 Unit cell: (104.76, 147.44, 130.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 57 16.00 P 55 15.00 O 3305 8.00 N 2922 7.00 C 10507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.59 Conformation dependent library (CDL) restraints added in 674.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " Number of angles added : 21 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 21 sheets defined 39.9% alpha, 18.0% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'C' and resid 15 through 32 Processing helix chain 'C' and resid 37 through 59 removed outlier: 4.002A pdb=" N LYS C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.681A pdb=" N SER C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 110 removed outlier: 3.896A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 107 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 136 removed outlier: 3.594A pdb=" N SER C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 Processing helix chain 'C' and resid 163 through 177 removed outlier: 4.330A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.888A pdb=" N LYS C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 208 through 223 removed outlier: 3.786A pdb=" N ALA C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 214 " --> pdb=" O HIS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.098A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.528A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR C 285 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 322 removed outlier: 3.754A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 333 Processing helix chain 'C' and resid 338 through 362 removed outlier: 4.131A pdb=" N TYR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 474 removed outlier: 3.635A pdb=" N CYS C 474 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 495 Processing helix chain 'C' and resid 509 through 513 removed outlier: 3.603A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 513 " --> pdb=" O PHE C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 513' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 547 through 552 removed outlier: 3.508A pdb=" N ASN C 552 " --> pdb=" O GLU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 572 Processing helix chain 'C' and resid 592 through 595 Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.770A pdb=" N VAL C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 631 No H-bonds generated for 'chain 'C' and resid 629 through 631' Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.774A pdb=" N ALA C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.730A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 removed outlier: 3.710A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.713A pdb=" N MET B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.529A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 225 removed outlier: 4.029A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 287 removed outlier: 4.012A pdb=" N ASP B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.262A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.504A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.680A pdb=" N LEU B 634 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.875A pdb=" N GLU B 693 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 740 Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 831 through 847 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 883 removed outlier: 3.679A pdb=" N THR B 883 " --> pdb=" O MET B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.613A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 removed outlier: 3.728A pdb=" N LYS B1398 " --> pdb=" O THR B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1421 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.192A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1492 removed outlier: 3.856A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1499 removed outlier: 3.800A pdb=" N GLU B1499 " --> pdb=" O LEU B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.873A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B1588 " --> pdb=" O GLN B1584 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B1597 " --> pdb=" O LYS B1593 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B1598 " --> pdb=" O GLY B1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 Processing helix chain 'B' and resid 1619 through 1629 removed outlier: 3.721A pdb=" N LEU B1628 " --> pdb=" O LYS B1624 " (cutoff:3.500A) Processing helix chain 'B' and resid 1662 through 1667 Processing helix chain 'B' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'C' and resid 425 through 431 removed outlier: 6.534A pdb=" N VAL C 401 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL C 487 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 403 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.490A pdb=" N VAL C 622 " --> pdb=" O VAL C 658 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR C 660 " --> pdb=" O VAL C 622 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU C 624 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 585 through 587 removed outlier: 4.256A pdb=" N HIS C 585 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.521A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.662A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.827A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 5.973A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 512 through 513 removed outlier: 4.788A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 512 through 513 removed outlier: 4.788A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.893A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB3, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB4, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.521A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.521A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLN B 673 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE B 868 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 675 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 866 " --> pdb=" O THR B 675 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU B 677 " --> pdb=" O ALA B 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 699 through 700 removed outlier: 7.147A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA B 791 " --> pdb=" O LEU B 800 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LYS B 802 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N HIS B 789 " --> pdb=" O LYS B 802 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N LYS B 804 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N ILE B 787 " --> pdb=" O LYS B 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB8, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB9, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.544A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.544A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B1517 " --> pdb=" O THR B 960 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR B 960 " --> pdb=" O VAL B1517 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER B1519 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 958 " --> pdb=" O SER B1519 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP B1521 " --> pdb=" O CYS B 956 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS B 956 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG B1523 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 954 " --> pdb=" O ARG B1523 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU B1525 " --> pdb=" O GLY B 952 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY B 952 " --> pdb=" O GLU B1525 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER B 951 " --> pdb=" O THR B1569 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B1569 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS B 953 " --> pdb=" O LEU B1567 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B1567 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 955 " --> pdb=" O ASP B1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 967 through 968 removed outlier: 4.449A pdb=" N LYS B 988 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.639A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 651 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2820 1.32 - 1.44: 4863 1.44 - 1.56: 9472 1.56 - 1.69: 102 1.69 - 1.81: 80 Bond restraints: 17337 Sorted by residual: bond pdb=" O3' G a 37 " pdb=" P G a 38 " ideal model delta sigma weight residual 1.607 1.511 0.096 1.20e-02 6.94e+03 6.39e+01 bond pdb=" O3' U a 40 " pdb=" P A a 41 " ideal model delta sigma weight residual 1.607 1.536 0.071 1.20e-02 6.94e+03 3.53e+01 bond pdb=" O3' G a 38 " pdb=" P G a 39 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.20e-02 6.94e+03 3.45e+01 bond pdb=" CA LEU B1672 " pdb=" C LEU B1672 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.14e-02 7.69e+03 3.39e+01 bond pdb=" CA GLU B1650 " pdb=" C GLU B1650 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.34e-02 5.57e+03 3.39e+01 ... (remaining 17332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 22844 2.46 - 4.91: 679 4.91 - 7.37: 87 7.37 - 9.82: 22 9.82 - 12.28: 3 Bond angle restraints: 23635 Sorted by residual: angle pdb=" N GLU B1650 " pdb=" CA GLU B1650 " pdb=" C GLU B1650 " ideal model delta sigma weight residual 110.80 98.52 12.28 2.13e+00 2.20e-01 3.32e+01 angle pdb=" C TYR B1645 " pdb=" N PRO B1646 " pdb=" CA PRO B1646 " ideal model delta sigma weight residual 120.21 114.69 5.52 9.60e-01 1.09e+00 3.31e+01 angle pdb=" C PHE C 111 " pdb=" N ASN C 112 " pdb=" CA ASN C 112 " ideal model delta sigma weight residual 123.93 132.73 -8.80 1.54e+00 4.22e-01 3.27e+01 angle pdb=" N VAL B1647 " pdb=" CA VAL B1647 " pdb=" C VAL B1647 " ideal model delta sigma weight residual 107.75 99.70 8.05 1.46e+00 4.69e-01 3.04e+01 angle pdb=" N LYS B1638 " pdb=" CA LYS B1638 " pdb=" C LYS B1638 " ideal model delta sigma weight residual 113.20 105.82 7.38 1.36e+00 5.41e-01 2.94e+01 ... (remaining 23630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8827 17.94 - 35.88: 1018 35.88 - 53.83: 296 53.83 - 71.77: 126 71.77 - 89.71: 32 Dihedral angle restraints: 10299 sinusoidal: 4714 harmonic: 5585 Sorted by residual: dihedral pdb=" C4' G r -17 " pdb=" C3' G r -17 " pdb=" C2' G r -17 " pdb=" C1' G r -17 " ideal model delta sinusoidal sigma weight residual 36.34 -38.53 74.88 1 3.10e+00 1.04e-01 7.38e+02 dihedral pdb=" C4' U r -8 " pdb=" C3' U r -8 " pdb=" C2' U r -8 " pdb=" C1' U r -8 " ideal model delta sinusoidal sigma weight residual 36.35 -37.97 74.31 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' G r 11 " pdb=" C3' G r 11 " pdb=" C2' G r 11 " pdb=" C1' G r 11 " ideal model delta sinusoidal sigma weight residual 36.34 -37.66 74.00 1 3.10e+00 1.04e-01 7.24e+02 ... (remaining 10296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1998 0.065 - 0.129: 384 0.129 - 0.194: 93 0.194 - 0.258: 63 0.258 - 0.323: 28 Chirality restraints: 2566 Sorted by residual: chirality pdb=" C3' A r -1 " pdb=" C4' A r -1 " pdb=" O3' A r -1 " pdb=" C2' A r -1 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASP C 490 " pdb=" N ASP C 490 " pdb=" C ASP C 490 " pdb=" CB ASP C 490 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C3' G r 11 " pdb=" C4' G r 11 " pdb=" O3' G r 11 " pdb=" C2' G r 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2563 not shown) Planarity restraints: 2840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B1668 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ASP B1668 " -0.062 2.00e-02 2.50e+03 pdb=" O ASP B1668 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B1669 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 962 " -0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 963 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 963 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 963 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B1457 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLY B1457 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY B1457 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL B1458 " -0.019 2.00e-02 2.50e+03 ... (remaining 2837 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3531 2.78 - 3.31: 14258 3.31 - 3.84: 28247 3.84 - 4.37: 33740 4.37 - 4.90: 57805 Nonbonded interactions: 137581 Sorted by model distance: nonbonded pdb=" O SER B1453 " pdb=" OG SER B1453 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C r 14 " model vdw 2.256 3.040 nonbonded pdb=" O PHE B1011 " pdb=" OG1 THR B1015 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR B 922 " pdb=" OH TYR B1663 " model vdw 2.310 3.040 nonbonded pdb=" O ASN B 179 " pdb=" O2' G r -3 " model vdw 2.311 3.040 ... (remaining 137576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.007 0.187 17353 Z= 0.362 Angle : 1.052 34.879 23656 Z= 0.535 Chirality : 0.070 0.323 2566 Planarity : 0.007 0.084 2840 Dihedral : 18.090 89.709 6709 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.95 % Favored : 94.84 % Rotamer: Outliers : 3.70 % Allowed : 12.27 % Favored : 84.03 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.15), residues: 1919 helix: -1.86 (0.14), residues: 692 sheet: 0.13 (0.30), residues: 260 loop : -2.04 (0.16), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 16 TYR 0.017 0.002 TYR C 607 PHE 0.022 0.002 PHE B 805 TRP 0.018 0.002 TRP C 278 HIS 0.007 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.33 (17337) covalent geometry : angle 0.96129 / 0.53 (23635) hydrogen bonds : bond 0.16209 / 10.23 ( 631) hydrogen bonds : angle 6.43471 / 4.49 ( 1868) metal coordination : bond 0.13146 / 8.40 ( 16) metal coordination : angle 14.35219 / 10.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 391 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: C 60 LYS cc_start: 0.7352 (pptt) cc_final: 0.6979 (pptt) REVERT: C 92 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8157 (mmmt) REVERT: C 128 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7824 (mt) REVERT: C 164 GLU cc_start: 0.7147 (tp30) cc_final: 0.6863 (tp30) REVERT: C 234 ASP cc_start: 0.7075 (t0) cc_final: 0.6797 (t0) REVERT: C 260 ARG cc_start: 0.6830 (mmm160) cc_final: 0.6572 (mmm160) REVERT: C 346 LYS cc_start: 0.7449 (mmmt) cc_final: 0.7175 (mmmt) REVERT: C 569 ASP cc_start: 0.7008 (t70) cc_final: 0.6699 (t0) REVERT: C 611 LEU cc_start: 0.8381 (tp) cc_final: 0.8127 (tp) REVERT: C 630 ASP cc_start: 0.7436 (m-30) cc_final: 0.7178 (m-30) REVERT: C 661 MET cc_start: 0.8281 (mtt) cc_final: 0.8005 (mtt) REVERT: B 6 MET cc_start: 0.7072 (ppp) cc_final: 0.6786 (ppp) REVERT: B 7 ASN cc_start: 0.7680 (p0) cc_final: 0.7166 (p0) REVERT: B 124 GLU cc_start: 0.7666 (mp0) cc_final: 0.7299 (mp0) REVERT: B 138 ASN cc_start: 0.7228 (m-40) cc_final: 0.6914 (m-40) REVERT: B 159 ASP cc_start: 0.7586 (t0) cc_final: 0.7040 (t0) REVERT: B 189 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (tmtm) REVERT: B 314 ASP cc_start: 0.7429 (t0) cc_final: 0.7058 (t0) REVERT: B 315 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7266 (mm-30) REVERT: B 357 LYS cc_start: 0.8207 (mtpt) cc_final: 0.8002 (mtpp) REVERT: B 373 GLU cc_start: 0.7267 (tp30) cc_final: 0.7028 (tp30) REVERT: B 616 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8000 (mm-40) REVERT: B 620 GLU cc_start: 0.6617 (mp0) cc_final: 0.6365 (mp0) REVERT: B 844 ASP cc_start: 0.7233 (m-30) cc_final: 0.6861 (m-30) REVERT: B 866 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 950 LEU cc_start: 0.8333 (mt) cc_final: 0.7998 (mp) REVERT: B 969 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8383 (m) REVERT: B 1410 SER cc_start: 0.8267 (t) cc_final: 0.8009 (m) REVERT: B 1488 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7754 (mtt90) REVERT: B 1492 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7558 (mm-40) REVERT: B 1584 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7494 (tp-100) REVERT: B 1595 TYR cc_start: 0.8216 (t80) cc_final: 0.8009 (t80) REVERT: B 1669 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7575 (ttpp) outliers start: 63 outliers final: 16 residues processed: 435 average time/residue: 0.1777 time to fit residues: 108.3850 Evaluate side-chains 371 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 348 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 554 GLN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1584 GLN Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1640 GLU Chi-restraints excluded: chain B residue 1651 GLU Chi-restraints excluded: chain B residue 1669 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 ASN C 194 ASN C 554 GLN C 559 GLN C 576 ASN C 602 ASN B 287 ASN B 335 GLN B 348 GLN B 365 ASN B 433 GLN B 712 ASN B 924 HIS B 980 ASN B1010 HIS B1448 ASN B1544 ASN B1604 ASN B1692 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103691 restraints weight = 24414.503| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.83 r_work: 0.3080 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17353 Z= 0.155 Angle : 0.864 12.271 23656 Z= 0.377 Chirality : 0.082 1.059 2566 Planarity : 0.005 0.066 2840 Dihedral : 13.037 156.783 2808 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 3.29 % Allowed : 15.62 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 1919 helix: 0.30 (0.18), residues: 701 sheet: 0.30 (0.30), residues: 269 loop : -1.65 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 476 TYR 0.017 0.001 TYR B 808 PHE 0.027 0.001 PHE C 184 TRP 0.012 0.001 TRP C 278 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (17337) covalent geometry : angle 0.85910 / 0.38 (23635) hydrogen bonds : bond 0.04066 / 2.62 ( 631) hydrogen bonds : angle 4.44704 / 3.11 ( 1868) metal coordination : bond 0.00580 / 0.39 ( 16) metal coordination : angle 3.15179 / 2.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 368 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7763 (mtmm) REVERT: C 68 PHE cc_start: 0.8200 (m-80) cc_final: 0.7582 (m-80) REVERT: C 92 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8189 (mmmt) REVERT: C 213 LYS cc_start: 0.7680 (tttt) cc_final: 0.7300 (tttt) REVERT: C 234 ASP cc_start: 0.7933 (t0) cc_final: 0.7593 (t0) REVERT: C 260 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7374 (mmm160) REVERT: C 263 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7657 (ttp80) REVERT: C 395 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 554 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6050 (tp40) REVERT: C 569 ASP cc_start: 0.7581 (t70) cc_final: 0.7113 (t0) REVERT: C 630 ASP cc_start: 0.7896 (m-30) cc_final: 0.7685 (m-30) REVERT: C 678 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6605 (tm-30) REVERT: B 6 MET cc_start: 0.7678 (ppp) cc_final: 0.7074 (ppp) REVERT: B 7 ASN cc_start: 0.8045 (p0) cc_final: 0.7608 (p0) REVERT: B 81 LYS cc_start: 0.8575 (ptpp) cc_final: 0.8373 (pttt) REVERT: B 124 GLU cc_start: 0.7982 (mp0) cc_final: 0.7652 (mp0) REVERT: B 138 ASN cc_start: 0.7774 (m-40) cc_final: 0.7458 (m-40) REVERT: B 159 ASP cc_start: 0.8109 (t0) cc_final: 0.7507 (t0) REVERT: B 285 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8040 (ttpp) REVERT: B 314 ASP cc_start: 0.7735 (t0) cc_final: 0.7355 (t0) REVERT: B 357 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8277 (ttmm) REVERT: B 409 GLU cc_start: 0.7769 (tp30) cc_final: 0.7160 (tp30) REVERT: B 423 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8210 (tttm) REVERT: B 640 SER cc_start: 0.8237 (p) cc_final: 0.7974 (m) REVERT: B 727 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.5608 (p90) REVERT: B 844 ASP cc_start: 0.7903 (m-30) cc_final: 0.7518 (m-30) REVERT: B 866 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 1006 MET cc_start: 0.8547 (ttp) cc_final: 0.8196 (ttp) REVERT: B 1410 SER cc_start: 0.8505 (t) cc_final: 0.8276 (m) REVERT: B 1488 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8176 (mtt90) REVERT: B 1492 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8126 (mm-40) REVERT: B 1584 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7889 (tp-100) outliers start: 56 outliers final: 26 residues processed: 400 average time/residue: 0.1676 time to fit residues: 94.9872 Evaluate side-chains 376 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 344 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 554 GLN Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1584 GLN Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 148 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 178 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 187 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 552 ASN B 942 HIS B1568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104595 restraints weight = 24391.916| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.81 r_work: 0.3125 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17353 Z= 0.138 Angle : 0.711 11.840 23656 Z= 0.324 Chirality : 0.065 0.816 2566 Planarity : 0.004 0.061 2840 Dihedral : 12.945 173.471 2781 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.29 % Allowed : 17.38 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 1919 helix: 1.25 (0.19), residues: 701 sheet: 0.46 (0.30), residues: 268 loop : -1.38 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.012 0.001 TYR C 607 PHE 0.027 0.001 PHE C 184 TRP 0.012 0.001 TRP C 278 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (17337) covalent geometry : angle 0.70704 / 0.32 (23635) hydrogen bonds : bond 0.03630 / 2.33 ( 631) hydrogen bonds : angle 4.09580 / 2.88 ( 1868) metal coordination : bond 0.00575 / 0.40 ( 16) metal coordination : angle 2.55531 / 1.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 353 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 PHE cc_start: 0.8252 (m-80) cc_final: 0.7751 (m-80) REVERT: C 92 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8207 (mmmt) REVERT: C 163 TYR cc_start: 0.8242 (m-10) cc_final: 0.7942 (m-10) REVERT: C 188 ILE cc_start: 0.8117 (pt) cc_final: 0.7817 (mm) REVERT: C 213 LYS cc_start: 0.7751 (tttt) cc_final: 0.7488 (ttmt) REVERT: C 234 ASP cc_start: 0.7931 (t0) cc_final: 0.7582 (t0) REVERT: C 260 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7392 (mmm160) REVERT: C 263 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7681 (ttp80) REVERT: C 467 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 569 ASP cc_start: 0.7603 (t70) cc_final: 0.7389 (t0) REVERT: C 615 LYS cc_start: 0.7321 (mptt) cc_final: 0.7024 (mptt) REVERT: C 630 ASP cc_start: 0.8000 (m-30) cc_final: 0.7798 (m-30) REVERT: B 6 MET cc_start: 0.7648 (ppp) cc_final: 0.6674 (ppp) REVERT: B 138 ASN cc_start: 0.7770 (m-40) cc_final: 0.7417 (m-40) REVERT: B 159 ASP cc_start: 0.8090 (t0) cc_final: 0.7612 (t0) REVERT: B 214 GLU cc_start: 0.7649 (tp30) cc_final: 0.7371 (tt0) REVERT: B 314 ASP cc_start: 0.7878 (t0) cc_final: 0.7527 (t0) REVERT: B 386 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7270 (p0) REVERT: B 423 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (tttm) REVERT: B 640 SER cc_start: 0.8302 (p) cc_final: 0.8014 (m) REVERT: B 727 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.5809 (p90) REVERT: B 738 ARG cc_start: 0.8570 (tpt170) cc_final: 0.8115 (mmt180) REVERT: B 844 ASP cc_start: 0.7910 (m-30) cc_final: 0.7332 (m-30) REVERT: B 879 MET cc_start: 0.7462 (mtm) cc_final: 0.7261 (mtt) REVERT: B 968 ASP cc_start: 0.8359 (t70) cc_final: 0.8118 (t0) REVERT: B 1006 MET cc_start: 0.8545 (ttp) cc_final: 0.8224 (ttp) REVERT: B 1410 SER cc_start: 0.8501 (t) cc_final: 0.8227 (m) REVERT: B 1488 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8130 (mtt90) REVERT: B 1584 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7738 (tp-100) outliers start: 56 outliers final: 33 residues processed: 390 average time/residue: 0.1661 time to fit residues: 91.4729 Evaluate side-chains 378 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1584 GLN Chi-restraints excluded: chain B residue 1627 LYS Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 118 optimal weight: 0.0470 chunk 161 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105177 restraints weight = 24219.572| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.81 r_work: 0.3142 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17353 Z= 0.125 Angle : 0.675 11.596 23656 Z= 0.309 Chirality : 0.061 0.723 2566 Planarity : 0.004 0.048 2840 Dihedral : 12.928 179.432 2776 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.17 % Allowed : 18.56 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 1919 helix: 1.68 (0.20), residues: 701 sheet: 0.61 (0.30), residues: 264 loop : -1.23 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 212 TYR 0.013 0.001 TYR C 607 PHE 0.019 0.001 PHE C 184 TRP 0.011 0.001 TRP C 443 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17337) covalent geometry : angle 0.67274 / 0.31 (23635) hydrogen bonds : bond 0.03386 / 2.18 ( 631) hydrogen bonds : angle 3.92992 / 2.76 ( 1868) metal coordination : bond 0.00556 / 0.38 ( 16) metal coordination : angle 2.07691 / 1.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 351 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8206 (mmmt) REVERT: C 138 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7901 (mm-30) REVERT: C 213 LYS cc_start: 0.7752 (tttt) cc_final: 0.7520 (tttt) REVERT: C 234 ASP cc_start: 0.7924 (t0) cc_final: 0.7578 (t0) REVERT: C 250 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7268 (mm) REVERT: C 260 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7416 (mmm160) REVERT: C 263 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7734 (ttp80) REVERT: C 467 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 566 SER cc_start: 0.8358 (p) cc_final: 0.8151 (m) REVERT: C 615 LYS cc_start: 0.7371 (mptt) cc_final: 0.6801 (mptt) REVERT: C 618 LYS cc_start: 0.7983 (mptt) cc_final: 0.7719 (mptt) REVERT: B 6 MET cc_start: 0.7611 (ppp) cc_final: 0.6666 (ppp) REVERT: B 138 ASN cc_start: 0.7820 (m-40) cc_final: 0.7463 (m-40) REVERT: B 159 ASP cc_start: 0.8027 (t0) cc_final: 0.7563 (t0) REVERT: B 182 ASP cc_start: 0.8135 (t0) cc_final: 0.7931 (t70) REVERT: B 214 GLU cc_start: 0.7675 (tp30) cc_final: 0.7422 (tt0) REVERT: B 285 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7549 (ttpt) REVERT: B 314 ASP cc_start: 0.7929 (t0) cc_final: 0.7553 (t0) REVERT: B 335 GLN cc_start: 0.7870 (mt0) cc_final: 0.7567 (mt0) REVERT: B 423 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (tttm) REVERT: B 640 SER cc_start: 0.8273 (p) cc_final: 0.7981 (m) REVERT: B 727 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6057 (p90) REVERT: B 788 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 844 ASP cc_start: 0.7857 (m-30) cc_final: 0.7434 (m-30) REVERT: B 968 ASP cc_start: 0.8387 (t70) cc_final: 0.8130 (t0) REVERT: B 985 LYS cc_start: 0.7718 (mttt) cc_final: 0.7514 (mtmm) REVERT: B 1006 MET cc_start: 0.8529 (ttp) cc_final: 0.8232 (ttp) REVERT: B 1492 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8061 (mm-40) outliers start: 54 outliers final: 33 residues processed: 383 average time/residue: 0.1702 time to fit residues: 92.5227 Evaluate side-chains 375 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1627 LYS Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 182 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 169 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1584 GLN B1617 HIS B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102194 restraints weight = 24359.321| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.84 r_work: 0.3094 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17353 Z= 0.180 Angle : 0.724 11.693 23656 Z= 0.332 Chirality : 0.065 0.731 2566 Planarity : 0.004 0.048 2840 Dihedral : 12.976 175.757 2772 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 3.52 % Allowed : 18.67 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1919 helix: 1.71 (0.20), residues: 701 sheet: 0.72 (0.30), residues: 263 loop : -1.20 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 212 TYR 0.016 0.001 TYR C 607 PHE 0.018 0.002 PHE C 184 TRP 0.012 0.001 TRP C 276 HIS 0.005 0.001 HIS B1418 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (17337) covalent geometry : angle 0.71999 / 0.33 (23635) hydrogen bonds : bond 0.03950 / 2.55 ( 631) hydrogen bonds : angle 4.05277 / 2.85 ( 1868) metal coordination : bond 0.00982 / 0.70 ( 16) metal coordination : angle 2.75066 / 1.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7632 (tp30) cc_final: 0.7420 (tp30) REVERT: C 45 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7586 (mt) REVERT: C 92 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8286 (mmtp) REVERT: C 213 LYS cc_start: 0.7751 (tttt) cc_final: 0.7517 (tttt) REVERT: C 234 ASP cc_start: 0.7950 (t0) cc_final: 0.7589 (t0) REVERT: C 257 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8529 (mmtt) REVERT: C 260 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7454 (mmm160) REVERT: C 263 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7730 (ttp80) REVERT: C 467 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 618 LYS cc_start: 0.8048 (mptt) cc_final: 0.7690 (mptt) REVERT: B 6 MET cc_start: 0.7672 (ppp) cc_final: 0.6867 (ppp) REVERT: B 138 ASN cc_start: 0.8014 (m-40) cc_final: 0.7778 (m-40) REVERT: B 159 ASP cc_start: 0.8049 (t0) cc_final: 0.7570 (t0) REVERT: B 314 ASP cc_start: 0.8002 (t0) cc_final: 0.7593 (t0) REVERT: B 409 GLU cc_start: 0.7555 (tp30) cc_final: 0.7328 (mm-30) REVERT: B 423 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8260 (tttm) REVERT: B 458 PHE cc_start: 0.8158 (m-80) cc_final: 0.7769 (m-80) REVERT: B 640 SER cc_start: 0.8332 (p) cc_final: 0.8040 (m) REVERT: B 687 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7489 (t) REVERT: B 727 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6224 (p90) REVERT: B 788 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7899 (p0) REVERT: B 844 ASP cc_start: 0.7857 (m-30) cc_final: 0.7470 (m-30) REVERT: B 968 ASP cc_start: 0.8354 (t70) cc_final: 0.8077 (t0) REVERT: B 1006 MET cc_start: 0.8527 (ttp) cc_final: 0.8235 (ttp) REVERT: B 1492 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8079 (mm-40) REVERT: B 1595 TYR cc_start: 0.8188 (t80) cc_final: 0.7983 (t80) REVERT: B 1617 HIS cc_start: 0.7736 (p-80) cc_final: 0.7453 (p90) outliers start: 60 outliers final: 36 residues processed: 384 average time/residue: 0.1754 time to fit residues: 94.6442 Evaluate side-chains 376 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 916 LYS Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1692 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 20.0000 chunk 154 optimal weight: 0.0270 chunk 169 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 111 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN B1584 GLN B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105058 restraints weight = 24235.405| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.81 r_work: 0.3126 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17353 Z= 0.123 Angle : 0.665 11.659 23656 Z= 0.306 Chirality : 0.060 0.700 2566 Planarity : 0.004 0.048 2840 Dihedral : 12.860 179.566 2772 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.29 % Allowed : 19.73 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1919 helix: 1.90 (0.20), residues: 701 sheet: 0.84 (0.31), residues: 261 loop : -1.11 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.012 0.001 TYR C 607 PHE 0.018 0.001 PHE C 184 TRP 0.013 0.001 TRP C 443 HIS 0.004 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17337) covalent geometry : angle 0.66170 / 0.31 (23635) hydrogen bonds : bond 0.03289 / 2.12 ( 631) hydrogen bonds : angle 3.88530 / 2.73 ( 1868) metal coordination : bond 0.00543 / 0.37 ( 16) metal coordination : angle 2.25764 / 1.80 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 345 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7542 (mt) REVERT: C 92 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8217 (mmmt) REVERT: C 138 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7858 (mm-30) REVERT: C 213 LYS cc_start: 0.7753 (tttt) cc_final: 0.7392 (tttt) REVERT: C 226 THR cc_start: 0.8593 (t) cc_final: 0.8290 (p) REVERT: C 234 ASP cc_start: 0.7932 (t0) cc_final: 0.7549 (t0) REVERT: C 260 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7438 (mmm160) REVERT: C 263 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7733 (ttp80) REVERT: C 467 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 615 LYS cc_start: 0.7225 (mptt) cc_final: 0.6574 (mptt) REVERT: C 618 LYS cc_start: 0.8055 (mptt) cc_final: 0.7767 (mptt) REVERT: B 6 MET cc_start: 0.7618 (ppp) cc_final: 0.6792 (ppp) REVERT: B 79 ASN cc_start: 0.8313 (m-40) cc_final: 0.7702 (t0) REVERT: B 138 ASN cc_start: 0.7900 (m-40) cc_final: 0.7536 (m-40) REVERT: B 159 ASP cc_start: 0.8011 (t0) cc_final: 0.7557 (t0) REVERT: B 182 ASP cc_start: 0.8130 (t0) cc_final: 0.7926 (t70) REVERT: B 285 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7689 (ttpt) REVERT: B 314 ASP cc_start: 0.7998 (t0) cc_final: 0.7579 (t0) REVERT: B 409 GLU cc_start: 0.7545 (tp30) cc_final: 0.7079 (mm-30) REVERT: B 423 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8223 (tttm) REVERT: B 458 PHE cc_start: 0.8149 (m-80) cc_final: 0.7747 (m-80) REVERT: B 640 SER cc_start: 0.8265 (p) cc_final: 0.7966 (m) REVERT: B 687 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7423 (t) REVERT: B 727 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6063 (p90) REVERT: B 788 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7895 (p0) REVERT: B 844 ASP cc_start: 0.7874 (m-30) cc_final: 0.7511 (m-30) REVERT: B 968 ASP cc_start: 0.8346 (t70) cc_final: 0.8073 (t0) REVERT: B 1006 MET cc_start: 0.8539 (ttp) cc_final: 0.8221 (ttp) REVERT: B 1492 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8066 (mm-40) REVERT: B 1521 ASP cc_start: 0.7831 (p0) cc_final: 0.7625 (p0) outliers start: 56 outliers final: 34 residues processed: 382 average time/residue: 0.1765 time to fit residues: 95.3316 Evaluate side-chains 379 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 114 optimal weight: 0.0040 chunk 132 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 0.0770 chunk 108 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 342 ASN C 602 ASN B1448 ASN B1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105513 restraints weight = 24159.868| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.85 r_work: 0.3129 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17353 Z= 0.116 Angle : 0.651 11.556 23656 Z= 0.301 Chirality : 0.058 0.686 2566 Planarity : 0.004 0.046 2840 Dihedral : 12.764 178.788 2772 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.94 % Allowed : 20.43 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1919 helix: 2.04 (0.20), residues: 702 sheet: 0.81 (0.31), residues: 268 loop : -1.02 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.011 0.001 TYR C 704 PHE 0.020 0.001 PHE C 184 TRP 0.012 0.001 TRP C 443 HIS 0.004 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (17337) covalent geometry : angle 0.64841 / 0.30 (23635) hydrogen bonds : bond 0.03193 / 2.06 ( 631) hydrogen bonds : angle 3.80996 / 2.68 ( 1868) metal coordination : bond 0.00564 / 0.39 ( 16) metal coordination : angle 2.20272 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8177 (mmmt) REVERT: C 213 LYS cc_start: 0.7752 (tttt) cc_final: 0.7405 (tttt) REVERT: C 234 ASP cc_start: 0.7939 (t0) cc_final: 0.7565 (t0) REVERT: C 257 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8394 (mmtm) REVERT: C 260 ARG cc_start: 0.7846 (mmm160) cc_final: 0.7455 (mmm160) REVERT: C 263 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7720 (ttp80) REVERT: C 395 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 615 LYS cc_start: 0.7088 (mptt) cc_final: 0.6871 (mptt) REVERT: B 6 MET cc_start: 0.7664 (ppp) cc_final: 0.6830 (ppp) REVERT: B 79 ASN cc_start: 0.8320 (m-40) cc_final: 0.7709 (t0) REVERT: B 124 GLU cc_start: 0.7957 (mp0) cc_final: 0.7756 (mp0) REVERT: B 159 ASP cc_start: 0.8016 (t0) cc_final: 0.7569 (t0) REVERT: B 285 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7739 (ttpt) REVERT: B 314 ASP cc_start: 0.7919 (t0) cc_final: 0.7497 (t0) REVERT: B 409 GLU cc_start: 0.7553 (tp30) cc_final: 0.7079 (mm-30) REVERT: B 412 GLU cc_start: 0.7511 (tp30) cc_final: 0.7239 (tp30) REVERT: B 423 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8192 (tttm) REVERT: B 458 PHE cc_start: 0.8172 (m-80) cc_final: 0.7731 (m-80) REVERT: B 640 SER cc_start: 0.8234 (p) cc_final: 0.7924 (m) REVERT: B 687 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7308 (t) REVERT: B 705 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8360 (mtm180) REVERT: B 715 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6972 (mm-30) REVERT: B 727 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6191 (p90) REVERT: B 788 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7880 (p0) REVERT: B 844 ASP cc_start: 0.7915 (m-30) cc_final: 0.7535 (m-30) REVERT: B 968 ASP cc_start: 0.8309 (t70) cc_final: 0.8034 (t0) REVERT: B 1006 MET cc_start: 0.8545 (ttp) cc_final: 0.8224 (ttp) REVERT: B 1485 ASN cc_start: 0.8428 (m-40) cc_final: 0.8095 (m110) REVERT: B 1492 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8056 (mm-40) outliers start: 50 outliers final: 35 residues processed: 383 average time/residue: 0.1702 time to fit residues: 91.7122 Evaluate side-chains 384 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 6 optimal weight: 0.6980 chunk 154 optimal weight: 0.0870 chunk 130 optimal weight: 0.0030 chunk 151 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 169 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 357 GLN B1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106557 restraints weight = 24210.416| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.80 r_work: 0.3157 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17353 Z= 0.112 Angle : 0.647 11.471 23656 Z= 0.299 Chirality : 0.057 0.683 2566 Planarity : 0.004 0.045 2840 Dihedral : 12.712 178.391 2772 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.64 % Allowed : 21.02 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1919 helix: 2.09 (0.20), residues: 702 sheet: 0.82 (0.31), residues: 269 loop : -0.99 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.012 0.001 TYR C 704 PHE 0.019 0.001 PHE B1691 TRP 0.012 0.001 TRP C 443 HIS 0.004 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17337) covalent geometry : angle 0.64415 / 0.30 (23635) hydrogen bonds : bond 0.03121 / 2.01 ( 631) hydrogen bonds : angle 3.79215 / 2.67 ( 1868) metal coordination : bond 0.00440 / 0.29 ( 16) metal coordination : angle 2.14930 / 1.68 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 348 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8187 (mmmt) REVERT: C 213 LYS cc_start: 0.7757 (tttt) cc_final: 0.7482 (ttmt) REVERT: C 218 LYS cc_start: 0.7908 (tptt) cc_final: 0.7574 (tptt) REVERT: C 226 THR cc_start: 0.8582 (t) cc_final: 0.8267 (p) REVERT: C 234 ASP cc_start: 0.7903 (t0) cc_final: 0.7528 (t0) REVERT: C 260 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7471 (mmm160) REVERT: C 263 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7737 (ttp80) REVERT: C 615 LYS cc_start: 0.7052 (mptt) cc_final: 0.6845 (mptt) REVERT: B 6 MET cc_start: 0.7622 (ppp) cc_final: 0.6778 (ppp) REVERT: B 79 ASN cc_start: 0.8306 (m-40) cc_final: 0.8093 (t0) REVERT: B 159 ASP cc_start: 0.7959 (t0) cc_final: 0.7545 (t0) REVERT: B 314 ASP cc_start: 0.7922 (t0) cc_final: 0.7514 (t0) REVERT: B 409 GLU cc_start: 0.7547 (tp30) cc_final: 0.7220 (mm-30) REVERT: B 412 GLU cc_start: 0.7489 (tp30) cc_final: 0.7252 (tp30) REVERT: B 423 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (tttm) REVERT: B 640 SER cc_start: 0.8231 (p) cc_final: 0.7910 (m) REVERT: B 687 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7262 (t) REVERT: B 727 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6161 (p90) REVERT: B 788 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7875 (p0) REVERT: B 844 ASP cc_start: 0.7879 (m-30) cc_final: 0.7480 (m-30) REVERT: B 968 ASP cc_start: 0.8287 (t70) cc_final: 0.8017 (t0) REVERT: B 1006 MET cc_start: 0.8549 (ttp) cc_final: 0.8226 (ttp) REVERT: B 1485 ASN cc_start: 0.8408 (m-40) cc_final: 0.8076 (m110) REVERT: B 1492 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8063 (mm-40) REVERT: B 1638 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6884 (mtmt) REVERT: B 1679 LYS cc_start: 0.8477 (mptt) cc_final: 0.8264 (mptt) outliers start: 45 outliers final: 35 residues processed: 378 average time/residue: 0.1636 time to fit residues: 87.5527 Evaluate side-chains 382 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 602 ASN B1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105741 restraints weight = 24187.453| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.80 r_work: 0.3155 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17353 Z= 0.127 Angle : 0.662 11.368 23656 Z= 0.306 Chirality : 0.058 0.656 2566 Planarity : 0.004 0.044 2840 Dihedral : 12.745 179.608 2772 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.70 % Allowed : 21.26 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1919 helix: 2.06 (0.20), residues: 702 sheet: 0.92 (0.31), residues: 267 loop : -1.00 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.012 0.001 TYR C 607 PHE 0.021 0.001 PHE C 184 TRP 0.011 0.001 TRP C 443 HIS 0.013 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17337) covalent geometry : angle 0.65841 / 0.31 (23635) hydrogen bonds : bond 0.03298 / 2.13 ( 631) hydrogen bonds : angle 3.82197 / 2.69 ( 1868) metal coordination : bond 0.00599 / 0.42 ( 16) metal coordination : angle 2.46221 / 1.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7534 (mt) REVERT: C 68 PHE cc_start: 0.8309 (m-80) cc_final: 0.7778 (m-80) REVERT: C 92 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8227 (mmmt) REVERT: C 136 ASP cc_start: 0.8290 (t0) cc_final: 0.7981 (t0) REVERT: C 213 LYS cc_start: 0.7752 (tttt) cc_final: 0.7516 (ttmt) REVERT: C 218 LYS cc_start: 0.7930 (tptt) cc_final: 0.7551 (tptt) REVERT: C 226 THR cc_start: 0.8587 (t) cc_final: 0.8269 (p) REVERT: C 234 ASP cc_start: 0.7904 (t0) cc_final: 0.7528 (t0) REVERT: C 257 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8467 (mmtm) REVERT: C 260 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7484 (mmm160) REVERT: C 263 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7760 (ttp80) REVERT: C 609 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8140 (mm-30) REVERT: B 6 MET cc_start: 0.7642 (ppp) cc_final: 0.6816 (ppp) REVERT: B 108 ARG cc_start: 0.8660 (ptm-80) cc_final: 0.8372 (ptt-90) REVERT: B 159 ASP cc_start: 0.7956 (t0) cc_final: 0.7548 (t0) REVERT: B 182 ASP cc_start: 0.8132 (t0) cc_final: 0.7923 (t70) REVERT: B 314 ASP cc_start: 0.7917 (t0) cc_final: 0.7517 (t0) REVERT: B 409 GLU cc_start: 0.7542 (tp30) cc_final: 0.7194 (mm-30) REVERT: B 423 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8220 (tttm) REVERT: B 458 PHE cc_start: 0.8084 (m-80) cc_final: 0.7773 (m-80) REVERT: B 640 SER cc_start: 0.8270 (p) cc_final: 0.7944 (m) REVERT: B 687 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7265 (t) REVERT: B 727 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6217 (p90) REVERT: B 788 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7848 (p0) REVERT: B 844 ASP cc_start: 0.7890 (m-30) cc_final: 0.7543 (m-30) REVERT: B 968 ASP cc_start: 0.8291 (t70) cc_final: 0.8016 (t0) REVERT: B 1006 MET cc_start: 0.8542 (ttp) cc_final: 0.8217 (ttp) REVERT: B 1485 ASN cc_start: 0.8399 (m-40) cc_final: 0.8070 (m110) REVERT: B 1492 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8081 (mm-40) REVERT: B 1638 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6918 (mtmt) outliers start: 46 outliers final: 33 residues processed: 381 average time/residue: 0.1546 time to fit residues: 83.3445 Evaluate side-chains 383 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1692 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 124 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 0.0040 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1617 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105821 restraints weight = 24078.468| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.80 r_work: 0.3157 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 17353 Z= 0.145 Angle : 0.820 59.123 23656 Z= 0.432 Chirality : 0.059 0.653 2566 Planarity : 0.004 0.044 2840 Dihedral : 12.739 179.608 2771 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.41 % Allowed : 21.55 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1919 helix: 2.07 (0.20), residues: 702 sheet: 0.93 (0.31), residues: 267 loop : -1.00 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.012 0.001 TYR C 607 PHE 0.020 0.001 PHE C 184 TRP 0.011 0.001 TRP C 443 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17337) covalent geometry : angle 0.81677 / 0.43 (23635) hydrogen bonds : bond 0.03282 / 2.12 ( 631) hydrogen bonds : angle 3.82804 / 2.70 ( 1868) metal coordination : bond 0.00558 / 0.39 ( 16) metal coordination : angle 2.45992 / 1.92 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7527 (mt) REVERT: C 68 PHE cc_start: 0.8310 (m-80) cc_final: 0.7772 (m-80) REVERT: C 92 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8226 (mmmt) REVERT: C 136 ASP cc_start: 0.8293 (t0) cc_final: 0.7983 (t0) REVERT: C 176 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8181 (mt) REVERT: C 213 LYS cc_start: 0.7777 (tttt) cc_final: 0.7572 (ttmt) REVERT: C 218 LYS cc_start: 0.7932 (tptt) cc_final: 0.7551 (tptt) REVERT: C 226 THR cc_start: 0.8587 (t) cc_final: 0.8270 (p) REVERT: C 234 ASP cc_start: 0.7902 (t0) cc_final: 0.7529 (t0) REVERT: C 257 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8469 (mmtm) REVERT: C 260 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7486 (mmm160) REVERT: C 263 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7762 (ttp80) REVERT: C 609 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: B 6 MET cc_start: 0.7640 (ppp) cc_final: 0.6822 (ppp) REVERT: B 108 ARG cc_start: 0.8659 (ptm-80) cc_final: 0.8370 (ptt-90) REVERT: B 159 ASP cc_start: 0.7952 (t0) cc_final: 0.7541 (t0) REVERT: B 182 ASP cc_start: 0.8121 (t0) cc_final: 0.7917 (t70) REVERT: B 314 ASP cc_start: 0.7919 (t0) cc_final: 0.7520 (t0) REVERT: B 423 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8225 (tttm) REVERT: B 458 PHE cc_start: 0.8086 (m-80) cc_final: 0.7772 (m-80) REVERT: B 640 SER cc_start: 0.8270 (p) cc_final: 0.7940 (m) REVERT: B 687 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7262 (t) REVERT: B 727 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6218 (p90) REVERT: B 788 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7856 (p0) REVERT: B 844 ASP cc_start: 0.7885 (m-30) cc_final: 0.7533 (m-30) REVERT: B 968 ASP cc_start: 0.8286 (t70) cc_final: 0.8012 (t0) REVERT: B 1006 MET cc_start: 0.8545 (ttp) cc_final: 0.8221 (ttp) REVERT: B 1485 ASN cc_start: 0.8399 (m-40) cc_final: 0.8064 (m110) REVERT: B 1492 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8086 (mm-40) REVERT: B 1638 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6925 (mtmt) outliers start: 41 outliers final: 31 residues processed: 371 average time/residue: 0.1774 time to fit residues: 92.5037 Evaluate side-chains 382 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 342 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1549 LEU Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1636 ASP Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 chunk 162 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN B1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105681 restraints weight = 24169.956| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.82 r_work: 0.3149 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 17353 Z= 0.145 Angle : 0.820 59.123 23656 Z= 0.432 Chirality : 0.059 0.653 2566 Planarity : 0.004 0.044 2840 Dihedral : 12.739 179.608 2771 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.41 % Allowed : 21.49 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1919 helix: 2.07 (0.20), residues: 702 sheet: 0.93 (0.31), residues: 267 loop : -1.00 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.012 0.001 TYR C 607 PHE 0.020 0.001 PHE C 184 TRP 0.011 0.001 TRP C 443 HIS 0.011 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17337) covalent geometry : angle 0.81676 / 0.43 (23635) hydrogen bonds : bond 0.03282 / 2.12 ( 631) hydrogen bonds : angle 3.82804 / 2.70 ( 1868) metal coordination : bond 0.00558 / 0.39 ( 16) metal coordination : angle 2.45992 / 1.92 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4210.75 seconds wall clock time: 72 minutes 59.64 seconds (4379.64 seconds total)