Starting phenix.real_space_refine on Fri Feb 16 23:36:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2024/7xt4_33439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2024/7xt4_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2024/7xt4_33439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2024/7xt4_33439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2024/7xt4_33439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2024/7xt4_33439.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 Residue "C ARG 16": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 681": "OE1" <-> "OE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B GLU 763": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B GLU 947": "OE1" <-> "OE2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B GLU 1002": "OE1" <-> "OE2" Residue "B GLU 1437": "OE1" <-> "OE2" Residue "B GLU 1504": "OE1" <-> "OE2" Residue "B GLU 1525": "OE1" <-> "OE2" Residue "B GLU 1529": "OE1" <-> "OE2" Residue "B PHE 1557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1600": "OE1" <-> "OE2" Residue "B GLU 1650": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'RNA': 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: {'RNA': 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: 8.94, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 5.66 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: 7.04 Time building geometry restraints manager: 7.25 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 1.50e-02 4.44e+03 4.09e+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 bond pdb=" CA TYR B1674 " pdb=" C TYR B1674 " ideal model delta sigma weight residual 1.525 1.452 0.073 1.37e-02 5.33e+03 2.85e+01 bond pdb=" N LYS C 59 " pdb=" CA LYS C 59 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.29e-02 6.01e+03 2.30e+01 ... (remaining 17332 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.81: 476 104.81 - 112.20: 8446 112.20 - 119.60: 6073 119.60 - 126.99: 8279 126.99 - 134.39: 361 Bond angle restraints: 23635 Sorted by residual: angle pdb=" O2' G a 38 " pdb=" C2' G a 38 " pdb=" C1' G a 38 " ideal model delta sigma weight residual 108.40 97.41 10.99 1.50e+00 4.44e-01 5.37e+01 angle pdb=" C4' U r -13 " pdb=" C3' U r -13 " pdb=" O3' U r -13 " ideal model delta sigma weight residual 113.00 104.27 8.73 1.50e+00 4.44e-01 3.39e+01 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 ... (remaining 23630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 10047 35.59 - 71.18: 398 71.18 - 106.77: 38 106.77 - 142.36: 2 142.36 - 177.95: 12 Dihedral angle restraints: 10497 sinusoidal: 4912 harmonic: 5585 Sorted by residual: dihedral pdb=" O4' U a 36 " pdb=" C1' U a 36 " pdb=" N1 U a 36 " pdb=" C2 U a 36 " ideal model delta sinusoidal sigma weight residual 200.00 29.47 170.53 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C r 12 " pdb=" C1' C r 12 " pdb=" N1 C r 12 " pdb=" C2 C r 12 " ideal model delta sinusoidal sigma weight residual 200.00 34.84 165.16 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' U r -10 " pdb=" C1' U r -10 " pdb=" N1 U r -10 " pdb=" C2 U r -10 " ideal model delta sinusoidal sigma weight residual 200.00 37.63 162.37 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 10494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2266 0.084 - 0.169: 274 0.169 - 0.253: 22 0.253 - 0.338: 3 0.338 - 0.422: 1 Chirality restraints: 2566 Sorted by residual: chirality pdb=" C3' U a 35 " pdb=" C4' U a 35 " pdb=" O3' U a 35 " pdb=" C2' U a 35 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" P A a 41 " pdb=" OP1 A a 41 " pdb=" OP2 A a 41 " pdb=" O5' A a 41 " both_signs ideal model delta sigma weight residual True 2.41 -2.08 0.33 2.00e-01 2.50e+01 2.77e+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 ... (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 2.440 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C r 14 " model vdw 2.256 2.440 nonbonded pdb=" O PHE B1011 " pdb=" OG1 THR B1015 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR B 922 " pdb=" OH TYR B1663 " model vdw 2.310 2.440 nonbonded pdb=" O ASN B 179 " pdb=" O2' G r -3 " model vdw 2.311 2.440 ... (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 ========== 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: 1.030 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: 5.270 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 52.820 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.006 0.096 17337 Z= 0.385 Angle : 0.906 12.277 23635 Z= 0.532 Chirality : 0.055 0.422 2566 Planarity : 0.007 0.084 2840 Dihedral : 19.002 177.950 6907 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP C 278 HIS 0.007 0.001 HIS B 727 PHE 0.022 0.002 PHE B 805 TYR 0.017 0.002 TYR C 607 ARG 0.010 0.001 ARG C 16 *********************** 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 fitting. rotamer outliers: 63 poor density : 391 time to evaluate : 1.852 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: 0.7148 (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: 0.6573 (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: 0.6364 (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: 0.3836 time to fit residues: 229.9997 Evaluate side-chains 371 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 348 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 167 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 942 HIS B 980 ASN B1010 HIS B1485 ASN ** B1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1604 ASN B1692 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17337 Z= 0.260 Angle : 0.584 7.507 23635 Z= 0.302 Chirality : 0.043 0.242 2566 Planarity : 0.005 0.066 2840 Dihedral : 18.397 177.957 3006 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 3.93 % Allowed : 16.03 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 1919 helix: 0.34 (0.18), residues: 701 sheet: 0.32 (0.30), residues: 264 loop : -1.60 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 278 HIS 0.010 0.001 HIS B 328 PHE 0.028 0.002 PHE C 184 TYR 0.015 0.001 TYR B 808 ARG 0.005 0.000 ARG B 846 *********************** 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 434 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 367 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: C 68 PHE cc_start: 0.8155 (m-80) cc_final: 0.7596 (m-80) REVERT: C 92 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8105 (mmtp) REVERT: C 213 LYS cc_start: 0.7561 (tttt) cc_final: 0.7167 (tttt) REVERT: C 234 ASP cc_start: 0.7207 (t0) cc_final: 0.6954 (t0) REVERT: C 257 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8342 (mmtm) REVERT: C 260 ARG cc_start: 0.6821 (mmm160) cc_final: 0.6528 (mmm160) REVERT: C 395 GLN cc_start: 0.6987 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 6 MET cc_start: 0.7319 (ppp) cc_final: 0.6210 (ppp) REVERT: B 108 ARG cc_start: 0.8348 (ptt90) cc_final: 0.8100 (ptt-90) REVERT: B 124 GLU cc_start: 0.7593 (mp0) cc_final: 0.7320 (mp0) REVERT: B 138 ASN cc_start: 0.7430 (m-40) cc_final: 0.7041 (m-40) REVERT: B 159 ASP cc_start: 0.7589 (t0) cc_final: 0.7068 (t0) REVERT: B 189 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7894 (tmtm) REVERT: B 214 GLU cc_start: 0.6768 (tp30) cc_final: 0.6529 (tt0) REVERT: B 314 ASP cc_start: 0.7500 (t0) cc_final: 0.7171 (t0) REVERT: B 357 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7925 (ttmm) REVERT: B 409 GLU cc_start: 0.6787 (tp30) cc_final: 0.6285 (tp30) REVERT: B 640 SER cc_start: 0.8178 (p) cc_final: 0.7920 (m) REVERT: B 727 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.5884 (p90) REVERT: B 738 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7712 (mmt180) REVERT: B 844 ASP cc_start: 0.7164 (m-30) cc_final: 0.6759 (m-30) REVERT: B 866 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8116 (mt) REVERT: B 1006 MET cc_start: 0.8163 (ttp) cc_final: 0.7788 (ttp) REVERT: B 1410 SER cc_start: 0.8266 (t) cc_final: 0.7964 (m) REVERT: B 1488 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7785 (mtt90) REVERT: B 1492 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7504 (mm-40) REVERT: B 1584 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7512 (tp-100) outliers start: 67 outliers final: 39 residues processed: 405 average time/residue: 0.3689 time to fit residues: 208.8059 Evaluate side-chains 388 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 344 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 143 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 351 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 586 ASN Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN 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 1422 THR Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1468 ILE 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 1671 ASN 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 99 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 978 GLN B1448 ASN B1485 ASN B1568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17337 Z= 0.197 Angle : 0.539 7.225 23635 Z= 0.278 Chirality : 0.041 0.234 2566 Planarity : 0.004 0.061 2840 Dihedral : 18.124 177.548 2986 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 3.93 % Allowed : 17.91 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 1919 helix: 1.23 (0.19), residues: 701 sheet: 0.50 (0.30), residues: 272 loop : -1.34 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 278 HIS 0.010 0.001 HIS B 328 PHE 0.028 0.001 PHE C 184 TYR 0.014 0.001 TYR C 607 ARG 0.007 0.000 ARG B 212 *********************** 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 425 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 358 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7459 (mt) REVERT: C 68 PHE cc_start: 0.8133 (m-80) cc_final: 0.7596 (m-80) REVERT: C 92 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8076 (mmmt) REVERT: C 188 ILE cc_start: 0.7986 (pt) cc_final: 0.7666 (mm) REVERT: C 213 LYS cc_start: 0.7516 (tttt) cc_final: 0.7092 (tttt) REVERT: C 234 ASP cc_start: 0.7219 (t0) cc_final: 0.6972 (t0) REVERT: C 260 ARG cc_start: 0.6772 (mmm160) cc_final: 0.6487 (mmm160) REVERT: C 467 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 538 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 6 MET cc_start: 0.7244 (ppp) cc_final: 0.6230 (ppp) REVERT: B 124 GLU cc_start: 0.7521 (mp0) cc_final: 0.7307 (mp0) REVERT: B 138 ASN cc_start: 0.7458 (m-40) cc_final: 0.7060 (m-40) REVERT: B 159 ASP cc_start: 0.7560 (t0) cc_final: 0.7094 (t0) REVERT: B 189 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7803 (tmtm) REVERT: B 285 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7616 (ttpt) REVERT: B 314 ASP cc_start: 0.7669 (t0) cc_final: 0.7362 (t0) REVERT: B 335 GLN cc_start: 0.7533 (mt0) cc_final: 0.7292 (mt0) REVERT: B 357 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7919 (ttmm) REVERT: B 373 GLU cc_start: 0.7131 (tp30) cc_final: 0.6518 (tt0) REVERT: B 640 SER cc_start: 0.8184 (p) cc_final: 0.7913 (m) REVERT: B 727 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.5848 (p90) REVERT: B 844 ASP cc_start: 0.7130 (m-30) cc_final: 0.6856 (m-30) REVERT: B 1006 MET cc_start: 0.8164 (ttp) cc_final: 0.7788 (ttp) REVERT: B 1410 SER cc_start: 0.8250 (t) cc_final: 0.7929 (m) REVERT: B 1438 ASN cc_start: 0.7666 (m-40) cc_final: 0.7404 (m-40) REVERT: B 1488 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7755 (mtt90) REVERT: B 1492 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7498 (mm-40) REVERT: B 1584 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7352 (tp-100) outliers start: 67 outliers final: 40 residues processed: 401 average time/residue: 0.3722 time to fit residues: 210.3789 Evaluate side-chains 389 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 343 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 140 CYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1455 THR Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1525 GLU Chi-restraints excluded: chain B residue 1572 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 1671 ASN 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 177 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17337 Z= 0.182 Angle : 0.530 7.846 23635 Z= 0.272 Chirality : 0.041 0.232 2566 Planarity : 0.004 0.049 2840 Dihedral : 18.018 177.395 2980 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 3.76 % Allowed : 19.14 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1919 helix: 1.65 (0.20), residues: 701 sheet: 0.63 (0.30), residues: 272 loop : -1.22 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 443 HIS 0.011 0.001 HIS B 328 PHE 0.020 0.001 PHE C 184 TYR 0.013 0.001 TYR C 607 ARG 0.008 0.000 ARG B 212 *********************** 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 415 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 351 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7486 (mt) REVERT: C 63 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7442 (mm) REVERT: C 68 PHE cc_start: 0.8143 (m-80) cc_final: 0.7544 (m-80) REVERT: C 92 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8064 (mmmt) REVERT: C 197 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6902 (mm-40) REVERT: C 213 LYS cc_start: 0.7533 (tttt) cc_final: 0.7142 (tttt) REVERT: C 234 ASP cc_start: 0.7220 (t0) cc_final: 0.6983 (t0) REVERT: C 250 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6960 (mm) REVERT: C 260 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6466 (mmm160) REVERT: C 538 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8221 (tp) REVERT: C 590 MET cc_start: 0.7824 (mmm) cc_final: 0.6974 (mmm) REVERT: B 6 MET cc_start: 0.7239 (ppp) cc_final: 0.6239 (ppp) REVERT: B 138 ASN cc_start: 0.7488 (m-40) cc_final: 0.7085 (m-40) REVERT: B 159 ASP cc_start: 0.7549 (t0) cc_final: 0.7068 (t0) REVERT: B 189 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7835 (tmtm) REVERT: B 314 ASP cc_start: 0.7739 (t0) cc_final: 0.7435 (t0) REVERT: B 335 GLN cc_start: 0.7585 (mt0) cc_final: 0.7365 (mt0) REVERT: B 357 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7919 (ttmm) REVERT: B 409 GLU cc_start: 0.6785 (tp30) cc_final: 0.6532 (mm-30) REVERT: B 640 SER cc_start: 0.8171 (p) cc_final: 0.7891 (m) REVERT: B 727 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.5913 (p90) REVERT: B 844 ASP cc_start: 0.7128 (m-30) cc_final: 0.6853 (m-30) REVERT: B 866 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 936 GLU cc_start: 0.6731 (tt0) cc_final: 0.6496 (tt0) REVERT: B 1006 MET cc_start: 0.8163 (ttp) cc_final: 0.7794 (ttp) REVERT: B 1438 ASN cc_start: 0.7602 (m-40) cc_final: 0.7377 (m-40) REVERT: B 1492 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7493 (mm-40) REVERT: B 1512 MET cc_start: 0.7966 (mtp) cc_final: 0.7611 (ttm) outliers start: 64 outliers final: 46 residues processed: 392 average time/residue: 0.3529 time to fit residues: 193.6113 Evaluate side-chains 395 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 340 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 148 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1411 ASP Chi-restraints excluded: chain B residue 1423 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1456 LEU 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 1671 ASN 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 159 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN B1584 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17337 Z= 0.207 Angle : 0.538 7.507 23635 Z= 0.275 Chirality : 0.041 0.227 2566 Planarity : 0.004 0.047 2840 Dihedral : 17.969 177.099 2976 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 4.11 % Allowed : 19.32 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1919 helix: 1.75 (0.20), residues: 702 sheet: 0.70 (0.31), residues: 271 loop : -1.15 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 443 HIS 0.011 0.001 HIS B 328 PHE 0.018 0.001 PHE C 184 TYR 0.013 0.001 TYR C 607 ARG 0.007 0.000 ARG B 212 *********************** 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 411 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 341 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7498 (mt) REVERT: C 59 LYS cc_start: 0.7400 (ttmm) cc_final: 0.6895 (tttp) REVERT: C 63 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7315 (mm) REVERT: C 68 PHE cc_start: 0.8163 (m-80) cc_final: 0.7606 (m-80) REVERT: C 92 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: C 166 ASP cc_start: 0.6814 (m-30) cc_final: 0.6568 (m-30) REVERT: C 184 PHE cc_start: 0.8128 (t80) cc_final: 0.7916 (t80) REVERT: C 213 LYS cc_start: 0.7541 (tttt) cc_final: 0.7160 (tttt) REVERT: C 234 ASP cc_start: 0.7230 (t0) cc_final: 0.6984 (t0) REVERT: C 257 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8369 (mmtm) REVERT: C 260 ARG cc_start: 0.6743 (mmm160) cc_final: 0.6472 (mmm160) REVERT: C 538 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8246 (tp) REVERT: C 590 MET cc_start: 0.7831 (mmm) cc_final: 0.6940 (mmm) REVERT: B 6 MET cc_start: 0.7218 (ppp) cc_final: 0.6274 (ppp) REVERT: B 138 ASN cc_start: 0.7568 (m-40) cc_final: 0.7133 (m-40) REVERT: B 159 ASP cc_start: 0.7528 (t0) cc_final: 0.7059 (t0) REVERT: B 189 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7851 (tmtm) REVERT: B 285 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7170 (ttpt) REVERT: B 314 ASP cc_start: 0.7777 (t0) cc_final: 0.7457 (t0) REVERT: B 335 GLN cc_start: 0.7633 (mt0) cc_final: 0.7400 (mt0) REVERT: B 357 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7912 (ttmm) REVERT: B 458 PHE cc_start: 0.7862 (m-80) cc_final: 0.7485 (m-80) REVERT: B 640 SER cc_start: 0.8190 (p) cc_final: 0.7903 (m) REVERT: B 727 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.5971 (p90) REVERT: B 844 ASP cc_start: 0.7120 (m-30) cc_final: 0.6871 (m-30) REVERT: B 1006 MET cc_start: 0.8160 (ttp) cc_final: 0.7792 (ttp) REVERT: B 1438 ASN cc_start: 0.7594 (m-40) cc_final: 0.7376 (m-40) REVERT: B 1492 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7499 (mm-40) REVERT: B 1512 MET cc_start: 0.7956 (mtp) cc_final: 0.7618 (ttm) outliers start: 70 outliers final: 44 residues processed: 390 average time/residue: 0.3654 time to fit residues: 198.0514 Evaluate side-chains 389 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 339 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 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 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1424 ASP Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1456 LEU 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 1671 ASN 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 64 optimal weight: 0.0030 chunk 172 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN B1584 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17337 Z= 0.190 Angle : 0.527 7.390 23635 Z= 0.270 Chirality : 0.041 0.223 2566 Planarity : 0.004 0.046 2840 Dihedral : 17.932 177.178 2976 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 3.58 % Allowed : 19.96 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1919 helix: 1.88 (0.20), residues: 702 sheet: 0.75 (0.31), residues: 271 loop : -1.10 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 443 HIS 0.011 0.001 HIS B 328 PHE 0.015 0.001 PHE C 184 TYR 0.013 0.001 TYR C 607 ARG 0.008 0.000 ARG B 212 *********************** 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 402 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 341 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7501 (mt) REVERT: C 92 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8071 (mmmt) REVERT: C 184 PHE cc_start: 0.8101 (t80) cc_final: 0.7873 (t80) REVERT: C 213 LYS cc_start: 0.7557 (tttt) cc_final: 0.7165 (tttt) REVERT: C 234 ASP cc_start: 0.7226 (t0) cc_final: 0.6982 (t0) REVERT: C 257 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8315 (mmtm) REVERT: C 260 ARG cc_start: 0.6727 (mmm160) cc_final: 0.6476 (mmm160) REVERT: C 538 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8258 (tp) REVERT: C 590 MET cc_start: 0.7811 (mmm) cc_final: 0.6912 (mmm) REVERT: B 6 MET cc_start: 0.7175 (ppp) cc_final: 0.6267 (ppp) REVERT: B 138 ASN cc_start: 0.7607 (m-40) cc_final: 0.7358 (m-40) REVERT: B 159 ASP cc_start: 0.7511 (t0) cc_final: 0.7069 (t0) REVERT: B 189 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7890 (tmtm) REVERT: B 314 ASP cc_start: 0.7724 (t0) cc_final: 0.7403 (t0) REVERT: B 335 GLN cc_start: 0.7642 (mt0) cc_final: 0.7413 (mt0) REVERT: B 357 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7914 (ttmm) REVERT: B 373 GLU cc_start: 0.6911 (tt0) cc_final: 0.6590 (tt0) REVERT: B 458 PHE cc_start: 0.7874 (m-80) cc_final: 0.7484 (m-80) REVERT: B 596 SER cc_start: 0.8626 (p) cc_final: 0.8333 (m) REVERT: B 640 SER cc_start: 0.8183 (p) cc_final: 0.7898 (m) REVERT: B 727 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6021 (p90) REVERT: B 844 ASP cc_start: 0.7123 (m-30) cc_final: 0.6868 (m-30) REVERT: B 879 MET cc_start: 0.7805 (mtt) cc_final: 0.7575 (mtm) REVERT: B 1006 MET cc_start: 0.8157 (ttp) cc_final: 0.7791 (ttp) REVERT: B 1492 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 1512 MET cc_start: 0.7935 (mtp) cc_final: 0.7629 (ttm) outliers start: 61 outliers final: 43 residues processed: 382 average time/residue: 0.3955 time to fit residues: 212.2158 Evaluate side-chains 384 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 336 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1423 THR Chi-restraints excluded: chain B residue 1424 ASP 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 1671 ASN Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN B 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17337 Z= 0.180 Angle : 0.525 7.328 23635 Z= 0.269 Chirality : 0.040 0.219 2566 Planarity : 0.004 0.045 2840 Dihedral : 17.901 177.295 2975 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 3.64 % Allowed : 20.08 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1919 helix: 1.94 (0.20), residues: 703 sheet: 0.81 (0.31), residues: 270 loop : -1.07 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 443 HIS 0.012 0.001 HIS B 328 PHE 0.015 0.001 PHE B1691 TYR 0.013 0.001 TYR C 607 ARG 0.008 0.000 ARG B 212 *********************** 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 400 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 338 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7485 (mt) REVERT: C 92 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8069 (mmmt) REVERT: C 184 PHE cc_start: 0.8092 (t80) cc_final: 0.7863 (t80) REVERT: C 213 LYS cc_start: 0.7545 (tttt) cc_final: 0.7223 (ttmt) REVERT: C 234 ASP cc_start: 0.7222 (t0) cc_final: 0.6979 (t0) REVERT: C 257 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8329 (mmtm) REVERT: C 260 ARG cc_start: 0.6710 (mmm160) cc_final: 0.6473 (mmm160) REVERT: C 538 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 6 MET cc_start: 0.7143 (ppp) cc_final: 0.6297 (ppp) REVERT: B 138 ASN cc_start: 0.7624 (m-40) cc_final: 0.7212 (m-40) REVERT: B 159 ASP cc_start: 0.7502 (t0) cc_final: 0.7077 (t0) REVERT: B 189 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7920 (tmtm) REVERT: B 314 ASP cc_start: 0.7733 (t0) cc_final: 0.7415 (t0) REVERT: B 357 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7911 (ttmm) REVERT: B 373 GLU cc_start: 0.6821 (tt0) cc_final: 0.6567 (tt0) REVERT: B 458 PHE cc_start: 0.7890 (m-80) cc_final: 0.7516 (m-80) REVERT: B 500 LEU cc_start: 0.8196 (mp) cc_final: 0.7901 (mp) REVERT: B 596 SER cc_start: 0.8618 (p) cc_final: 0.8335 (m) REVERT: B 640 SER cc_start: 0.8180 (p) cc_final: 0.7893 (m) REVERT: B 727 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.5980 (p90) REVERT: B 844 ASP cc_start: 0.7120 (m-30) cc_final: 0.6853 (m-30) REVERT: B 879 MET cc_start: 0.7803 (mtt) cc_final: 0.7567 (mtm) REVERT: B 908 HIS cc_start: 0.7448 (t-170) cc_final: 0.7171 (t70) REVERT: B 1006 MET cc_start: 0.8151 (ttp) cc_final: 0.7811 (ttp) REVERT: B 1485 ASN cc_start: 0.7985 (m-40) cc_final: 0.7654 (m110) REVERT: B 1492 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7504 (mm-40) REVERT: B 1512 MET cc_start: 0.7918 (mtp) cc_final: 0.7619 (ttm) outliers start: 62 outliers final: 46 residues processed: 378 average time/residue: 0.3700 time to fit residues: 194.5652 Evaluate side-chains 387 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 336 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 179 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1423 THR Chi-restraints excluded: chain B residue 1424 ASP 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 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 1671 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN B1448 ASN B1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17337 Z= 0.248 Angle : 0.559 7.588 23635 Z= 0.287 Chirality : 0.042 0.217 2566 Planarity : 0.004 0.045 2840 Dihedral : 17.922 176.892 2975 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 3.52 % Allowed : 20.55 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1919 helix: 1.87 (0.20), residues: 702 sheet: 0.82 (0.31), residues: 270 loop : -1.09 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 443 HIS 0.012 0.001 HIS B 328 PHE 0.023 0.002 PHE B1691 TYR 0.015 0.001 TYR C 607 ARG 0.009 0.000 ARG B 212 *********************** 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 400 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 340 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7505 (mt) REVERT: C 92 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8112 (mmtp) REVERT: C 184 PHE cc_start: 0.8117 (t80) cc_final: 0.7893 (t80) REVERT: C 234 ASP cc_start: 0.7225 (t0) cc_final: 0.6983 (t0) REVERT: C 257 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8260 (mmtm) REVERT: C 260 ARG cc_start: 0.6720 (mmm160) cc_final: 0.6491 (mmm160) REVERT: C 538 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 6 MET cc_start: 0.7092 (ppp) cc_final: 0.6420 (ppp) REVERT: B 159 ASP cc_start: 0.7505 (t0) cc_final: 0.7074 (t0) REVERT: B 285 LYS cc_start: 0.7543 (ttpt) cc_final: 0.7307 (ttmm) REVERT: B 314 ASP cc_start: 0.7803 (t0) cc_final: 0.7482 (t0) REVERT: B 458 PHE cc_start: 0.7901 (m-80) cc_final: 0.7519 (m-80) REVERT: B 596 SER cc_start: 0.8646 (p) cc_final: 0.8360 (m) REVERT: B 640 SER cc_start: 0.8236 (p) cc_final: 0.7949 (m) REVERT: B 727 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6174 (p90) REVERT: B 844 ASP cc_start: 0.7074 (m-30) cc_final: 0.6828 (m-30) REVERT: B 908 HIS cc_start: 0.7484 (t-170) cc_final: 0.7202 (t70) REVERT: B 1006 MET cc_start: 0.8142 (ttp) cc_final: 0.7793 (ttp) REVERT: B 1485 ASN cc_start: 0.7995 (m-40) cc_final: 0.7669 (m110) REVERT: B 1492 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7505 (mm-40) REVERT: B 1679 LYS cc_start: 0.8240 (mptt) cc_final: 0.8019 (mptt) outliers start: 60 outliers final: 47 residues processed: 382 average time/residue: 0.3717 time to fit residues: 197.1802 Evaluate side-chains 385 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 334 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1423 THR Chi-restraints excluded: chain B residue 1424 ASP 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 1525 GLU 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 1671 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 166 optimal weight: 0.0020 chunk 177 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1617 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17337 Z= 0.201 Angle : 0.541 7.462 23635 Z= 0.277 Chirality : 0.041 0.219 2566 Planarity : 0.004 0.045 2840 Dihedral : 17.885 177.125 2971 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 3.23 % Allowed : 21.37 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1919 helix: 1.92 (0.20), residues: 701 sheet: 0.85 (0.31), residues: 270 loop : -1.08 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.012 0.001 HIS B 328 PHE 0.016 0.001 PHE B1691 TYR 0.014 0.001 TYR C 607 ARG 0.009 0.000 ARG B 212 *********************** 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 392 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 337 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7493 (mt) REVERT: C 92 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8163 (mmtp) REVERT: C 138 GLU cc_start: 0.7704 (mp0) cc_final: 0.7452 (mp0) REVERT: C 176 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8126 (mt) REVERT: C 184 PHE cc_start: 0.8095 (t80) cc_final: 0.7878 (t80) REVERT: C 234 ASP cc_start: 0.7214 (t0) cc_final: 0.6981 (t0) REVERT: C 257 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8308 (mmtm) REVERT: C 260 ARG cc_start: 0.6720 (mmm160) cc_final: 0.6482 (mmm160) REVERT: C 538 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 6 MET cc_start: 0.7046 (ppp) cc_final: 0.6432 (ppp) REVERT: B 159 ASP cc_start: 0.7516 (t0) cc_final: 0.7092 (t0) REVERT: B 285 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7435 (ttpt) REVERT: B 314 ASP cc_start: 0.7741 (t0) cc_final: 0.7395 (t0) REVERT: B 458 PHE cc_start: 0.7875 (m-80) cc_final: 0.7523 (m-80) REVERT: B 500 LEU cc_start: 0.8192 (mp) cc_final: 0.7904 (mp) REVERT: B 596 SER cc_start: 0.8639 (p) cc_final: 0.8338 (m) REVERT: B 640 SER cc_start: 0.8210 (p) cc_final: 0.7918 (m) REVERT: B 715 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6587 (mm-30) REVERT: B 727 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6100 (p90) REVERT: B 844 ASP cc_start: 0.7126 (m-30) cc_final: 0.6877 (m-30) REVERT: B 908 HIS cc_start: 0.7489 (t-170) cc_final: 0.7204 (t70) REVERT: B 1006 MET cc_start: 0.8143 (ttp) cc_final: 0.7795 (ttp) REVERT: B 1485 ASN cc_start: 0.7985 (m-40) cc_final: 0.7654 (m110) REVERT: B 1492 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7509 (mm-40) REVERT: B 1512 MET cc_start: 0.7920 (mtp) cc_final: 0.7646 (ttm) REVERT: B 1679 LYS cc_start: 0.8212 (mptt) cc_final: 0.8011 (mptt) outliers start: 55 outliers final: 45 residues processed: 374 average time/residue: 0.3837 time to fit residues: 198.6863 Evaluate side-chains 382 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 332 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1423 THR Chi-restraints excluded: chain B residue 1424 ASP 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 1525 GLU 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 1671 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1617 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17337 Z= 0.182 Angle : 0.531 7.372 23635 Z= 0.273 Chirality : 0.041 0.214 2566 Planarity : 0.004 0.046 2840 Dihedral : 17.825 177.107 2971 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 3.05 % Allowed : 21.37 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1919 helix: 1.94 (0.20), residues: 702 sheet: 0.88 (0.31), residues: 270 loop : -1.06 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.012 0.001 HIS B 328 PHE 0.012 0.001 PHE B 546 TYR 0.023 0.001 TYR B1595 ARG 0.009 0.000 ARG B 212 ********************** 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 387 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 335 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7455 (mt) REVERT: C 92 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8047 (mmmt) REVERT: C 176 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8101 (mt) REVERT: C 184 PHE cc_start: 0.8081 (t80) cc_final: 0.7832 (t80) REVERT: C 234 ASP cc_start: 0.7226 (t0) cc_final: 0.6974 (t0) REVERT: C 257 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8316 (mmtm) REVERT: C 260 ARG cc_start: 0.6724 (mmm160) cc_final: 0.6499 (mmm160) REVERT: C 538 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8262 (tp) REVERT: C 590 MET cc_start: 0.7777 (mmm) cc_final: 0.7110 (mmm) REVERT: B 6 MET cc_start: 0.7023 (ppp) cc_final: 0.6429 (ppp) REVERT: B 159 ASP cc_start: 0.7474 (t0) cc_final: 0.7127 (t0) REVERT: B 314 ASP cc_start: 0.7741 (t0) cc_final: 0.7422 (t0) REVERT: B 458 PHE cc_start: 0.7868 (m-80) cc_final: 0.7504 (m-80) REVERT: B 500 LEU cc_start: 0.8185 (mp) cc_final: 0.7888 (mp) REVERT: B 596 SER cc_start: 0.8614 (p) cc_final: 0.8325 (m) REVERT: B 640 SER cc_start: 0.8182 (p) cc_final: 0.7873 (m) REVERT: B 727 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6085 (p90) REVERT: B 844 ASP cc_start: 0.7106 (m-30) cc_final: 0.6850 (m-30) REVERT: B 908 HIS cc_start: 0.7447 (t-170) cc_final: 0.7155 (t70) REVERT: B 1006 MET cc_start: 0.8147 (ttp) cc_final: 0.7793 (ttp) REVERT: B 1485 ASN cc_start: 0.7987 (m-40) cc_final: 0.7650 (m110) REVERT: B 1492 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7505 (mm-40) REVERT: B 1596 GLN cc_start: 0.7805 (mp10) cc_final: 0.7535 (mp10) outliers start: 52 outliers final: 45 residues processed: 368 average time/residue: 0.3764 time to fit residues: 191.7038 Evaluate side-chains 382 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 332 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 81 THR 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 249 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 764 SER 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 1423 THR Chi-restraints excluded: chain B residue 1424 ASP 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 1525 GLU 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 167 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.0060 chunk 138 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3439 r_free = 0.3439 target = 0.117021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101244 restraints weight = 24018.888| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.82 r_work: 0.3064 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17337 Z= 0.180 Angle : 0.533 12.280 23635 Z= 0.273 Chirality : 0.040 0.212 2566 Planarity : 0.004 0.045 2840 Dihedral : 17.783 177.087 2968 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 2.99 % Allowed : 21.67 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1919 helix: 1.98 (0.20), residues: 702 sheet: 0.95 (0.31), residues: 270 loop : -1.05 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.013 0.001 HIS B 328 PHE 0.013 0.001 PHE C 254 TYR 0.021 0.001 TYR B1595 ARG 0.009 0.000 ARG B 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.36 seconds wall clock time: 81 minutes 57.30 seconds (4917.30 seconds total)