Starting phenix.real_space_refine on Thu Nov 16 21:58:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/11_2023/7xt4_33439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/11_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_33439/11_2023/7xt4_33439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/11_2023/7xt4_33439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/11_2023/7xt4_33439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt4_33439/11_2023/7xt4_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 9.07, per 1000 atoms: 0.54 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: 6.52 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: 5.19 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: 6.75 Time building geometry restraints manager: 7.02 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 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.390 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 51.190 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.390 ------------------------------------------------------------------------------- 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 : 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 % 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 *********************** 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 : 1.968 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 16 residues processed: 435 average time/residue: 0.3816 time to fit residues: 229.7688 Evaluate side-chains 364 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 348 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1816 time to fit residues: 7.7263 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17337 Z= 0.275 Angle : 0.600 7.426 23635 Z= 0.311 Chirality : 0.043 0.249 2566 Planarity : 0.005 0.067 2840 Dihedral : 15.020 177.466 2753 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 3.23 % Allowed : 16.38 % Favored : 80.39 % 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: -0.91 (0.17), residues: 1919 helix: 0.31 (0.18), residues: 701 sheet: 0.31 (0.30), residues: 265 loop : -1.60 (0.17), residues: 953 *********************** 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 422 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 367 time to evaluate : 1.995 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 31 residues processed: 395 average time/residue: 0.3672 time to fit residues: 203.4367 Evaluate side-chains 373 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 342 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2014 time to fit residues: 13.5130 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 978 GLN B1448 ASN B1568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17337 Z= 0.200 Angle : 0.550 7.362 23635 Z= 0.284 Chirality : 0.041 0.236 2566 Planarity : 0.004 0.061 2840 Dihedral : 14.912 177.655 2753 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 2.11 % Allowed : 18.50 % Favored : 79.39 % 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: 1.24 (0.19), residues: 701 sheet: 0.51 (0.30), residues: 272 loop : -1.34 (0.18), residues: 946 *********************** 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 402 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 366 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 390 average time/residue: 0.3805 time to fit residues: 207.6939 Evaluate side-chains 360 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 343 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1628 time to fit residues: 7.8026 ------------------------------------------------------------------------------- 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: 1.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 chunk 120 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2122 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= 0.163 Angle : 0.526 7.142 23635 Z= 0.270 Chirality : 0.040 0.230 2566 Planarity : 0.004 0.050 2840 Dihedral : 14.828 177.568 2753 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 1.76 % Allowed : 19.85 % Favored : 78.39 % 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: 0.28 (0.19), residues: 1919 helix: 1.71 (0.20), residues: 701 sheet: 0.70 (0.31), residues: 270 loop : -1.18 (0.18), residues: 948 *********************** 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 380 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 350 time to evaluate : 1.875 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 370 average time/residue: 0.3961 time to fit residues: 206.0294 Evaluate side-chains 358 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 343 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1981 time to fit residues: 7.8255 ------------------------------------------------------------------------------- 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: 0.7980 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17337 Z= 0.217 Angle : 0.545 7.599 23635 Z= 0.280 Chirality : 0.041 0.225 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.848 177.065 2753 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 1.12 % Allowed : 20.55 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.19), residues: 1919 helix: 1.78 (0.20), residues: 702 sheet: 0.73 (0.31), residues: 272 loop : -1.12 (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 364 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 345 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 356 average time/residue: 0.3820 time to fit residues: 188.3662 Evaluate side-chains 345 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1652 time to fit residues: 4.4906 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2331 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= 0.250 Angle : 0.563 7.885 23635 Z= 0.289 Chirality : 0.042 0.224 2566 Planarity : 0.004 0.046 2840 Dihedral : 14.853 177.031 2753 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 1.76 % Allowed : 20.73 % Favored : 77.51 % 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: 0.42 (0.19), residues: 1919 helix: 1.82 (0.20), residues: 696 sheet: 0.80 (0.31), residues: 270 loop : -1.09 (0.19), residues: 953 *********************** 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 366 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 336 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 354 average time/residue: 0.4059 time to fit residues: 199.1570 Evaluate side-chains 347 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 330 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2173 time to fit residues: 8.8478 ------------------------------------------------------------------------------- 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: 4.9990 chunk 21 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 161 optimal weight: 0.0000 chunk 106 optimal weight: 0.0370 chunk 190 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17337 Z= 0.148 Angle : 0.523 7.346 23635 Z= 0.268 Chirality : 0.040 0.219 2566 Planarity : 0.004 0.045 2840 Dihedral : 14.737 177.317 2753 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 0.76 % Allowed : 21.49 % Favored : 77.75 % 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: 0.60 (0.19), residues: 1919 helix: 2.02 (0.20), residues: 696 sheet: 0.79 (0.31), residues: 272 loop : -1.01 (0.19), residues: 951 *********************** 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: 13 poor density : 339 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 346 average time/residue: 0.4033 time to fit residues: 192.9567 Evaluate side-chains 336 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 332 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2601 time to fit residues: 4.8631 ------------------------------------------------------------------------------- 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: 0.4980 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 908 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17337 Z= 0.184 Angle : 0.534 7.530 23635 Z= 0.274 Chirality : 0.040 0.213 2566 Planarity : 0.004 0.045 2840 Dihedral : 14.745 177.114 2753 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 0.94 % Allowed : 22.25 % Favored : 76.81 % 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: 0.62 (0.19), residues: 1919 helix: 2.02 (0.20), residues: 697 sheet: 0.83 (0.31), residues: 272 loop : -0.99 (0.19), residues: 950 *********************** 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 352 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 336 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 342 average time/residue: 0.4014 time to fit residues: 189.9206 Evaluate side-chains 342 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 330 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1929 time to fit residues: 6.5729 ------------------------------------------------------------------------------- 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: 0.2980 chunk 182 optimal weight: 0.8980 chunk 166 optimal weight: 0.0040 chunk 177 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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: 0.7634 moved from start: 0.2529 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= 0.160 Angle : 0.524 7.401 23635 Z= 0.269 Chirality : 0.040 0.208 2566 Planarity : 0.004 0.044 2840 Dihedral : 14.686 176.845 2753 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 0.41 % Allowed : 22.25 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.19), residues: 1919 helix: 2.10 (0.20), residues: 697 sheet: 0.85 (0.31), residues: 272 loop : -0.94 (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 339 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 332 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 339 average time/residue: 0.3920 time to fit residues: 183.9940 Evaluate side-chains 327 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1603 time to fit residues: 2.9683 ------------------------------------------------------------------------------- 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: 1.9990 chunk 114 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 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: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17337 Z= 0.297 Angle : 0.594 7.614 23635 Z= 0.305 Chirality : 0.043 0.204 2566 Planarity : 0.004 0.045 2840 Dihedral : 14.828 176.489 2753 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 0.53 % Allowed : 23.08 % Favored : 76.39 % 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: 0.49 (0.19), residues: 1919 helix: 1.85 (0.20), residues: 697 sheet: 0.85 (0.31), residues: 270 loop : -1.04 (0.19), residues: 952 ********************** 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 345 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 341 average time/residue: 0.4104 time to fit residues: 195.8257 Evaluate side-chains 337 residues out of total 1703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 334 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1888 time to fit residues: 3.6673 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 ASN B 834 HIS B 978 GLN B1448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097972 restraints weight = 24456.428| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.81 r_work: 0.2985 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17337 Z= 0.422 Angle : 0.669 8.557 23635 Z= 0.343 Chirality : 0.047 0.217 2566 Planarity : 0.005 0.048 2840 Dihedral : 14.975 176.638 2753 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 0.59 % Allowed : 23.66 % Favored : 75.75 % 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: 0.16 (0.19), residues: 1919 helix: 1.49 (0.20), residues: 700 sheet: 0.74 (0.31), residues: 266 loop : -1.18 (0.18), residues: 953 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.15 seconds wall clock time: 81 minutes 0.13 seconds (4860.13 seconds total)