Starting phenix.real_space_refine (version: dev) on Wed Feb 22 07:43:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2023/7xt4_33439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2023/7xt4_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_2023/7xt4_33439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2023/7xt4_33439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2023/7xt4_33439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/02_2023/7xt4_33439.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9.39, per 1000 atoms: 0.56 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: 6.61 Conformation dependent library (CDL) restraints added in 2.3 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: 4.77 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: 7.17 Time building geometry restraints manager: 7.07 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: 9934 35.59 - 71.18: 327 71.18 - 106.77: 24 106.77 - 142.36: 2 142.36 - 177.95: 12 Dihedral angle restraints: 10299 sinusoidal: 4714 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 10296 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 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. 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: 1.040 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: 5.900 Check model and map are aligned: 0.230 Process input model: 51.420 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 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 : 17.941 177.950 6709 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 % 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 *********************** 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 : 1.915 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 16 residues processed: 435 average time/residue: 0.3805 time to fit residues: 229.8423 Evaluate side-chains 364 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 348 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1881 time to fit residues: 7.7839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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 ** B1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1584 GLN B1604 ASN B1692 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 17337 Z= 0.274 Angle : 0.597 7.419 23635 Z= 0.309 Chirality : 0.043 0.249 2566 Planarity : 0.005 0.067 2840 Dihedral : 15.018 177.678 2753 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer Outliers : 3.35 % 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: 0.31 (0.18), residues: 701 sheet: 0.34 (0.30), residues: 264 loop : -1.59 (0.17), residues: 954 *********************** 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 425 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 368 time to evaluate : 2.077 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 398 average time/residue: 0.3795 time to fit residues: 210.9535 Evaluate side-chains 377 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 343 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1944 time to fit residues: 14.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 0.0030 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN B 978 GLN B1448 ASN B1568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17337 Z= 0.180 Angle : 0.540 7.343 23635 Z= 0.279 Chirality : 0.041 0.233 2566 Planarity : 0.004 0.061 2840 Dihedral : 14.889 177.651 2753 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer Outliers : 1.94 % 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: -0.13 (0.18), residues: 1919 helix: 1.24 (0.19), residues: 701 sheet: 0.53 (0.30), residues: 268 loop : -1.34 (0.18), residues: 950 *********************** 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 392 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 359 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 381 average time/residue: 0.3766 time to fit residues: 201.3013 Evaluate side-chains 349 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 336 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1622 time to fit residues: 6.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 120 optimal weight: 0.5980 chunk 180 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 chunk 171 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 GLN C 503 ASN B 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 17337 Z= 0.157 Angle : 0.520 7.182 23635 Z= 0.267 Chirality : 0.040 0.228 2566 Planarity : 0.004 0.050 2840 Dihedral : 14.808 177.410 2753 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.67 % Rotamer Outliers : 2.17 % 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: 0.31 (0.19), residues: 1919 helix: 1.75 (0.20), residues: 701 sheet: 0.66 (0.31), residues: 272 loop : -1.17 (0.18), residues: 946 *********************** 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 384 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 347 time to evaluate : 2.083 Fit side-chains outliers start: 37 outliers final: 18 residues processed: 370 average time/residue: 0.3894 time to fit residues: 203.8158 Evaluate side-chains 360 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 342 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1877 time to fit residues: 8.6882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 17337 Z= 0.270 Angle : 0.572 7.884 23635 Z= 0.293 Chirality : 0.043 0.227 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.880 176.771 2753 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer Outliers : 1.41 % 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: 1.73 (0.20), residues: 702 sheet: 0.72 (0.31), residues: 272 loop : -1.14 (0.18), residues: 945 *********************** 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 366 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 342 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 358 average time/residue: 0.4009 time to fit residues: 199.8263 Evaluate side-chains 346 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 337 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2094 time to fit residues: 6.0930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 17337 Z= 0.314 Angle : 0.597 7.962 23635 Z= 0.307 Chirality : 0.044 0.230 2566 Planarity : 0.004 0.048 2840 Dihedral : 14.915 176.998 2753 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.89 % Rotamer Outliers : 1.76 % 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: 0.27 (0.19), residues: 1919 helix: 1.61 (0.20), residues: 702 sheet: 0.71 (0.31), residues: 270 loop : -1.12 (0.19), residues: 947 *********************** 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 372 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 342 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 358 average time/residue: 0.3874 time to fit residues: 193.6668 Evaluate side-chains 353 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 332 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2400 time to fit residues: 11.1501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 5.9990 chunk 21 optimal weight: 0.0470 chunk 109 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 0.0370 chunk 106 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN B 908 HIS ** B1671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17337 Z= 0.167 Angle : 0.536 7.731 23635 Z= 0.276 Chirality : 0.040 0.222 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.768 177.537 2753 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.41 % Rotamer Outliers : 0.94 % 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: 0.52 (0.19), residues: 1919 helix: 1.93 (0.20), residues: 696 sheet: 0.73 (0.31), residues: 271 loop : -1.01 (0.19), residues: 952 *********************** 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 352 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 336 time to evaluate : 2.016 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 346 average time/residue: 0.4072 time to fit residues: 196.0857 Evaluate side-chains 335 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 330 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1716 time to fit residues: 4.1409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 503 ASN B 913 GLN ** B1671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17337 Z= 0.229 Angle : 0.559 7.155 23635 Z= 0.288 Chirality : 0.042 0.218 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.787 177.033 2753 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer Outliers : 1.23 % 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: 0.48 (0.19), residues: 1919 helix: 1.87 (0.20), residues: 697 sheet: 0.75 (0.31), residues: 270 loop : -1.04 (0.19), residues: 952 *********************** 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 355 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 334 time to evaluate : 1.887 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 346 average time/residue: 0.3867 time to fit residues: 186.8572 Evaluate side-chains 344 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2264 time to fit residues: 7.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 0.0870 chunk 166 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 0.0370 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17337 Z= 0.171 Angle : 0.539 6.588 23635 Z= 0.279 Chirality : 0.040 0.212 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.708 177.328 2753 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer Outliers : 0.53 % 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: 0.57 (0.19), residues: 1919 helix: 1.96 (0.20), residues: 697 sheet: 0.77 (0.31), residues: 272 loop : -1.00 (0.19), residues: 950 *********************** 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 338 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 329 time to evaluate : 1.866 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 336 average time/residue: 0.3977 time to fit residues: 185.7513 Evaluate side-chains 327 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1793 time to fit residues: 3.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 17337 Z= 0.413 Angle : 0.650 8.408 23635 Z= 0.335 Chirality : 0.047 0.218 2566 Planarity : 0.004 0.047 2840 Dihedral : 14.912 176.655 2753 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.68 % Rotamer Outliers : 0.65 % 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: 1.54 (0.20), residues: 700 sheet: 0.72 (0.31), residues: 266 loop : -1.14 (0.18), residues: 953 ********************** 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 344 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 333 time to evaluate : 1.890 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 338 average time/residue: 0.4063 time to fit residues: 191.2695 Evaluate side-chains 340 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 333 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2115 time to fit residues: 5.1264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 541 ASN B 908 HIS B 993 ASN B1448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100653 restraints weight = 24220.951| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.74 r_work: 0.3070 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17337 Z= 0.225 Angle : 0.578 8.153 23635 Z= 0.299 Chirality : 0.042 0.210 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.786 177.400 2753 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer Outliers : 0.41 % 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: 0.35 (0.19), residues: 1919 helix: 1.68 (0.20), residues: 700 sheet: 0.83 (0.31), residues: 261 loop : -1.08 (0.19), residues: 958 =============================================================================== Job complete usr+sys time: 4233.14 seconds wall clock time: 76 minutes 57.45 seconds (4617.45 seconds total)